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vprusa/PV269-cvic1.pl

Last active March 18, 2021 10:22
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# PV269 - cvic1 - pipeline for simulation E.coli reads and so on ...
Raw
hist.log
START-assembly_stats
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.hist.log
29386
11236
11112
10693
10627
10361
10291
9944
10191
9893 =
9851 =
9959 =
9587 =
9575 =
9505 =
9576 =
9594 =
9457 =
9502 =
9560 ==
9489 ==
9381 ==
9442 ==
9328 ==
9242 ==
9019 ==
8950 ==
8922 ==
8943 ==
62713 ===
6442 ===
18674 ===
18262 ===
17957 ===
17573 ===
17204 ===
16918 ===
16588 ===
16212 ===
15880 ====
15435 ====
14992 ====
14616 ====
14224 ====
13840 ====
13505 ====
13306 ====
12617 ====
12566 ====
12201 =====
11916 =====
11414 =====
10902 =====
10591 =====
10274 =====
10006 =====
9774 =====
9423 =====
9102 =====
1003187 ======
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.hist.log
29386
11236
11112
10693
10627
10361
10291
9944
10191
9893 =
9851 =
9959 =
9587 =
9575 =
9505 =
9576 =
9594 =
9457 =
9502 =
9560 ==
9489 ==
9381 ==
9442 ==
9328 ==
9242 ==
9019 ==
8950 ==
8922 ==
8943 ==
62713 ===
6442 ===
18674 ===
18262 ===
17957 ===
17573 ===
17204 ===
16918 ===
16588 ===
16212 ===
15880 ====
15435 ====
14992 ====
14616 ====
14224 ====
13840 ====
13505 ====
13306 ====
12617 ====
12566 ====
12201 =====
11916 =====
11414 =====
10902 =====
10591 =====
10274 =====
10006 =====
9774 =====
9423 =====
9102 =====
1003187 ======
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.hist.log
22707
8328
8311
7982
7788
7594
7477
7246
7501
7215 =
7206 =
7444 =
7182 =
7260 =
7166 =
7265 =
7381 =
7228 =
7361 =
7460 ==
7473 ==
7409 ==
7482 ==
7488 ==
7438 ==
7281 ==
7243 ==
7308 ==
7296 ==
6211 ===
6149 ===
12978 ===
12438 ===
12469 ===
11993 ===
11771 ===
11634 ===
11433 ===
11113 ===
10962 ====
10592 ====
10342 ====
9999 ====
9853 ====
9513 ====
9165 ====
9020 ====
8627 ====
8558 ====
8280 =====
8055 =====
7687 =====
7352 =====
7163 =====
6896 =====
6619 =====
6512 =====
6174 =====
6140 =====
625914 ======
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.hist.log
441
453
415
484
442
442
434
434
412
348 =
358 =
373 =
369 =
361 =
382 =
353 =
318 =
339 =
310 =
288 ==
319 ==
303 ==
308 ==
283 ==
287 ==
298 ==
293 ==
278 ==
257 ==
265 ===
275 ===
695 ===
598 ===
643 ===
562 ===
580 ===
570 ===
562 ===
549 ===
532 ====
1635 ====
596 ====
569 ====
592 ====
567 ====
568 ====
565 ====
564 ====
576 ====
563 =====
488 =====
472 =====
526 =====
500 =====
503 =====
464 =====
504 =====
412 =====
434 =====
85204 ======
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.hist.log
441
453
415
484
442
442
434
434
412
348 =
358 =
373 =
369 =
361 =
382 =
353 =
318 =
339 =
310 =
288 ==
319 ==
303 ==
308 ==
283 ==
287 ==
298 ==
293 ==
278 ==
257 ==
265 ===
275 ===
695 ===
598 ===
643 ===
562 ===
580 ===
570 ===
562 ===
549 ===
532 ====
1635 ====
596 ====
569 ====
592 ====
567 ====
568 ====
565 ====
564 ====
576 ====
563 =====
488 =====
472 =====
526 =====
500 =====
503 =====
464 =====
504 =====
412 =====
434 =====
85204 ======
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.hist.log
488
477
533
435
480
472
442
419
408
438 =
417 =
390 =
389 =
390 =
438 =
416 =
394 =
366 =
371 =
360 ==
346 ==
330 ==
334 ==
340 ==
348 ==
317 ==
313 ==
318 ==
329 ==
348 ===
318 ===
669 ===
679 ===
722 ===
624 ===
697 ===
643 ===
631 ===
607 ===
631 ====
2149 ====
661 ====
642 ====
623 ====
610 ====
586 ====
636 ====
585 ====
663 ====
600 =====
608 =====
549 =====
555 =====
547 =====
571 =====
604 =====
529 =====
543 =====
535 =====
94825 ======
AR=( "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa" );
for i in ${AR[@]} ; do echo "F: $i"; assembly_stats $i > $i.ass.out; done
Raw
PV269-cvic1.pl
#!/usr/bin/perl
# PV269 - cvic1 - pipeline for simulation E.coli reads and so on ...
# https://is.muni.cz/auth/el/fi/jaro2021/PV269/index.qwarp?prejit=6672020
use Cwd;
my $cwd = getcwd();
# note: https://github.com/vprusa/MUNI-2018-iv110-iv114-proj
# this variable is used for skipping commands executed in previous run
# my $conf = "cws";
my $conf = "cwsval";
# my $conf = "al";
# wgsim -N value .. for testing smaller=>faste pipeline
# my $wgsN = 15000;
# my $wgsN = 5000000;
my $wgsN = 50000;
# my $wgsN = 234983650;
my $cmd = "";
my $HEAD_CMD = "head -n5";
sub myExec {
print "\e[37m@_\n\e[0m" ;
# system("@_ >/dev/null 2>&1");
system("@_");
print "";
}
if($conf =~ m/c/){
print "\e[32mSTART\e[0m\n";
$cmd = "cd $cwd ; rm ./wgsim/out* ; rm ./sample/sample.out ; rm ./sample/sample.out";
print "\e[37m$cmd\n\e[0m" ;
# system($cmd);
}
#############################################################
# wgsim https://github.com/lh3/wgsim
#############################################################
# wgsim https://github.com/lh3/wgsim simulate short reads (150bp) from E.coli, 50x coverage, error rate 0.5% and 5%, paired (d=2000bp) and unpaired
my $rlen = 150;
my $FILE = "./GCF_000005845.2_ASM584v2_genomic.fna";
my $OUT_PREFIX = "";
# my @paired = ("paired", "unpaired");
my @paired = ("2000", "0");
my @er = ("0.5", "0.05");
if($conf =~ m/w/){
print "\e[32mSTART\e[0m-wgsim\n";
foreach ( @paired ) {
my $p = $_;
foreach ( @er ) {
$OUT_PREFIX = "out_paired_$p.er_$_.";
print "OUT_PREFIX: $OUT_PREFIX\n";
$cmd = "cd $cwd/wgsim ; ./wgsim -N$wgsN -1$rlen -2$rlen -d$p -e$_ ${FILE} ${OUT_PREFIX}1.fq ${OUT_PREFIX}2.fq > /dev/null ; ${HEAD_CMD} ${OUT_PREFIX}1.fq "; # ls -lh
myExec $cmd;
# print "\e[37m$cmd\n\e[0m" ;
# system($cmd);
print "\n";
}
}
}
#############################################################
# sample https://github.com/alexpreynolds/sample
#############################################################
# sample https://github.com/alexpreynolds/sample subsample one of the four combinations (coordinate with each other) fastaq (create 1x and 8x coverage)
print "\e[32mSTART\e[0m-sample\n";
# my $FILE_NAME = "$cwd/wgsim/out_paired_".@paired[0].".er_".@er[1].".1.fq";
my $FILE_NAME = "out_paired_".@paired[0].".er_0.05.1.fq";
my $FILE_PATH = "$cwd/wgsim/$FILE_NAME";
# idk why does this show
# my $FILE_NAME = "$cwd/wgsim/out_paired_".@paired[0].".er_".@er[0].".1.fq";
my @cov = ("1", "8");
my $rows = `wc -l < $FILE_PATH`;
$rows = $rows / 4;
if($conf =~ m/s/){
foreach ( @cov ) {
my $c = $_;
print "$c\n";
# print "echo \$(($rows * $_))";
my $sampleSize = `echo \$(($rows * $c))`;
chomp $sampleSize;
my $SAMPLE_OUT="$cwd/sample/sample.c_$c.out";
$cmd = "cd $cwd/sample ; ./sample --sample-size=$sampleSize --lines-per-offset=4 $FILE_PATH > $SAMPLE_OUT ; ${HEAD_CMD} $SAMPLE_OUT";
myExec $cmd;
}
}
#############################################################
# velvet
#############################################################
# velvet (velveth, velvetg) https://www.ebi.ac.uk/~zerbino/velvet/ assemble the three sets of reads at 3 coverages using two values of k (31, 51)
# https://www.biostars.org/p/44211/
# ```make 'MAXKMERLENGTH=92'```
my @covV = ("31", "51");
print "\e[32mSTART\e[0m-velvet\n";
if($conf =~ m/v/) {
for(@covV) {
$cv = $_;
for(@cov) {
$c = $_;
print "\e[32mSTART\e[0m-velveth\n";
my $FILES = "$cwd/sample/sample.c_$c.out $cwd/wgsim/out_paired_".@paired[0].".er_".@er[1].".1.fq";
myExec "cd $cwd/velvet ; ./velveth ./ $cv -fastq $FILES ; ${$HEAD_CMD}";
print "\e[32mSTART\e[0m-velvetg\n";
$cmd = "cd $cwd/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500";
myExec $cmd;
$cmd = "cd $cwd/velvet ; mv ./contigs.fa ./contigs.c_".$c.".cv_".$cv.".fa";
myExec $cmd;
}
print "\e[32mSTART\e[0m-velveth\n";
# my $FILE = "$cwd/wgsim/out_paired_".@paired[0].".er_0.05.1.fq";
myExec "cd $cwd/velvet ; ./velveth ./ $cv -fastq $FILE_PATH ; ${$HEAD_CMD}";
print "\e[32mSTART\e[0m-velvetg\n";
$cmd = "cd $cwd/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500";
myExec $cmd;
$cmd = "cd $cwd/velvet ; mv ./contigs.fa ./contigs.c_$c.cv_$cv.$FILE_NAME.fa";
myExec $cmd;
}
}
my $HIST_FILE="hist.log";
my $CDATA_FILE="contigs.data.fa";
my $CLDATA_FILE="contigs.data.len.fa";
my $HIST_DIVISOR = 10;
#############################################################
# assembly_stats
#############################################################
# assembly_stats https://github.com/MikeTrizna/assembly_stats calculate N50, show histogram of contig lengths (gnuplot?, hist() or ggplot2 in R?)
sub myAss {
if($conf =~ m/l/){
print "\e[32mSTART\e[0m-histogram-of-contig-lengths\n";
my $cmd = "cd $cwd/velvet/ ; grep -v '>' @_ > @_.contigs.data.fa ; awk '{ print \"\\t\"length(\$0); }' @_.$CDATA_FILE | sort | uniq -c | sort -k2,2 -n > @_.$CLDATA_FILE ; perl -lane 'print \$F[0], \"\\t\", \"=\" x (\$F[1] / $HIST_DIVISOR)' @_.$CLDATA_FILE > @_.$HIST_FILE ; cat @_.$HIST_FILE";
print("$cmd\n");
system($cmd);
}
}
my @FILES = ("out_paired_".@paired[0].".er_0.05.1.fq", "out_paired_".@paired[1].".er_0.05.1.fq");
my $execDirAssembly = "/home/studentx99/.local/lib/python3.8/site-packages/assembly_stats/";
# executed manually
if($conf =~ m/a/) {
print "\e[32mSTART\e[0m-assembly_stats\n";
for(@covV) {
$cv = $_;
for(@cov) {
$c = $_;
# ./contigs.c_$c.cv_$cv.$FILE_NAME.fa;
# ./contigs.c_".$c.".cv_".$cv.".fa;
myExec $cmd;
my $f = "$cwd/velvet/contigs.c_".$c.".cv_".$cv.".fa";
myExec "assembly_stats $f";
myAss $f;
}
my $f = "$cwd/velvet/contigs.c_$c.cv_$cv.$FILE_NAME.fa";
myExec "assembly_stats $f";
myAss $f;
}
print("AR=( ");
for(@covV) {
$cv = $_;
my $f = "";
for(@cov) {
$c = $_;
$f = "$cwd/velvet/contigs.c_".$c.".cv_".$cv.".fa";
print('"'.$f.'" ');
}
$f = "$cwd/velvet/contigs.c_$c.cv_$cv.$FILE_NAME.fa";
print('"'.$f.'" ');
}
print(');');
print("\n");
print('for i in ${AR[@]} ; do echo "F: $i"; assembly_stats $i > $i.ass.out; done');
print("\n");
}
#
Raw
results-assembly_stats-whole.log
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.ass.out
{
"Contig Stats": {
"L10": 2623,
"L20": 6444,
"L30": 10629,
"L40": 14814,
"L50": 18999,
"N10": 204,
"N20": 150,
"N30": 150,
"N40": 150,
"N50": 150,
"gc_content": 50.733513508519344,
"longest": 499,
"mean": 148.0774166155588,
"median": 150.0,
"sequence_count": 42394,
"shortest": 61,
"total_bps": 6277594
},
"Scaffold Stats": {
"L10": 2623,
"L20": 6444,
"L30": 10629,
"L40": 14814,
"L50": 18999,
"N10": 204,
"N20": 150,
"N30": 150,
"N40": 150,
"N50": 150,
"gc_content": 50.733513508519344,
"longest": 499,
"mean": 148.0774166155588,
"median": 150.0,
"sequence_count": 42394,
"shortest": 61,
"total_bps": 6277594
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.ass.out
{
"Contig Stats": {
"L10": 2623,
"L20": 6444,
"L30": 10629,
"L40": 14814,
"L50": 18999,
"N10": 204,
"N20": 150,
"N30": 150,
"N40": 150,
"N50": 150,
"gc_content": 50.733513508519344,
"longest": 499,
"mean": 148.0774166155588,
"median": 150.0,
"sequence_count": 42394,
"shortest": 61,
"total_bps": 6277594
},
"Scaffold Stats": {
"L10": 2623,
"L20": 6444,
"L30": 10629,
"L40": 14814,
"L50": 18999,
"N10": 204,
"N20": 150,
"N30": 150,
"N40": 150,
"N50": 150,
"gc_content": 50.733513508519344,
"longest": 499,
"mean": 148.0774166155588,
"median": 150.0,
"sequence_count": 42394,
"shortest": 61,
"total_bps": 6277594
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.ass.out
{
"Contig Stats": {
"L10": 557,
"L20": 1247,
"L30": 2042,
"L40": 2967,
"L50": 3995,
"N10": 236,
"N20": 204,
"N30": 177,
"N40": 151,
"N50": 143,
"gc_content": 50.75029902862806,
"longest": 499,
"mean": 142.2227760015046,
"median": 131.0,
"sequence_count": 10634,
"shortest": 61,
"total_bps": 1512397
},
"Scaffold Stats": {
"L10": 557,
"L20": 1247,
"L30": 2042,
"L40": 2967,
"L50": 3995,
"N10": 236,
"N20": 204,
"N30": 177,
"N40": 151,
"N50": 143,
"gc_content": 50.75029902862806,
"longest": 499,
"mean": 142.2227760015046,
"median": 131.0,
"sequence_count": 10634,
"shortest": 61,
"total_bps": 1512397
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.ass.out
{
"Contig Stats": {
"L10": 13,
"L20": 27,
"L30": 41,
"L40": 56,
"L50": 72,
"N10": 247,
"N20": 236,
"N30": 230,
"N40": 224,
"N50": 211,
"gc_content": 51.6534236971255,
"longest": 369,
"mean": 203.76190476190476,
"median": 203.0,
"sequence_count": 168,
"shortest": 143,
"total_bps": 34232
},
"Scaffold Stats": {
"L10": 13,
"L20": 27,
"L30": 41,
"L40": 56,
"L50": 72,
"N10": 247,
"N20": 236,
"N30": 230,
"N40": 224,
"N50": 211,
"gc_content": 51.6534236971255,
"longest": 369,
"mean": 203.76190476190476,
"median": 203.0,
"sequence_count": 168,
"shortest": 143,
"total_bps": 34232
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.ass.out
{
"Contig Stats": {
"L10": 13,
"L20": 27,
"L30": 41,
"L40": 56,
"L50": 72,
"N10": 247,
"N20": 236,
"N30": 230,
"N40": 224,
"N50": 211,
"gc_content": 51.6534236971255,
"longest": 369,
"mean": 203.76190476190476,
"median": 203.0,
"sequence_count": 168,
"shortest": 143,
"total_bps": 34232
},
"Scaffold Stats": {
"L10": 13,
"L20": 27,
"L30": 41,
"L40": 56,
"L50": 72,
"N10": 247,
"N20": 236,
"N30": 230,
"N40": 224,
"N50": 211,
"gc_content": 51.6534236971255,
"longest": 369,
"mean": 203.76190476190476,
"median": 203.0,
"sequence_count": 168,
"shortest": 143,
"total_bps": 34232
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.ass.out
{
"Contig Stats": {
"L10": 29,
"L20": 62,
"L30": 97,
"L40": 133,
"L50": 172,
"N10": 234,
"N20": 220,
"N30": 209,
"N40": 198,
"N50": 189,
"gc_content": 51.15349535919309,
"longest": 339,
"mean": 189.2284263959391,
"median": 185.0,
"sequence_count": 394,
"shortest": 143,
"total_bps": 74556
},
"Scaffold Stats": {
"L10": 29,
"L20": 62,
"L30": 97,
"L40": 133,
"L50": 172,
"N10": 234,
"N20": 220,
"N30": 209,
"N40": 198,
"N50": 189,
"gc_content": 51.15349535919309,
"longest": 339,
"mean": 189.2284263959391,
"median": 185.0,
"sequence_count": 394,
"shortest": 143,
"total_bps": 74556
}
}
####################################
# my $wgsN = 1500000;
####################################
for i in ${AR[@]} ; do echo "F: $i"; python ./cli.py $i > $i.ass.out; cat $i.ass.out; done
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa
ok
{
"Contig Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 378,
"N20": 378,
"N30": 378,
"N40": 378,
"N50": 378,
"gc_content": 0,
"longest": 378,
"mean": 108.69443089038433,
"median": 106.0,
"sequence_count": 766478,
"shortest": 61,
"total_bps": 83311890
},
"Scaffold Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 378,
"N20": 378,
"N30": 378,
"N40": 378,
"N50": 378,
"gc_content": 0,
"longest": 378,
"mean": 108.69443089038433,
"median": 106.0,
"sequence_count": 766478,
"shortest": 61,
"total_bps": 83311890
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa
ok
{
"Contig Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 378,
"N20": 378,
"N30": 378,
"N40": 378,
"N50": 378,
"gc_content": 0,
"longest": 378,
"mean": 108.69443089038433,
"median": 106.0,
"sequence_count": 766478,
"shortest": 61,
"total_bps": 83311890
},
"Scaffold Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 378,
"N20": 378,
"N30": 378,
"N40": 378,
"N50": 378,
"gc_content": 0,
"longest": 378,
"mean": 108.69443089038433,
"median": 106.0,
"sequence_count": 766478,
"shortest": 61,
"total_bps": 83311890
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa
ok
{
"Contig Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 321,
"N20": 321,
"N30": 321,
"N40": 321,
"N50": 321,
"gc_content": 0,
"longest": 321,
"mean": 102.66954801103411,
"median": 101.0,
"sequence_count": 512955,
"shortest": 61,
"total_bps": 52664858
},
"Scaffold Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 321,
"N20": 321,
"N30": 321,
"N40": 321,
"N50": 321,
"gc_content": 0,
"longest": 321,
"mean": 102.66954801103411,
"median": 101.0,
"sequence_count": 512955,
"shortest": 61,
"total_bps": 52664858
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa
ok
{
"Contig Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 1107,
"N20": 1107,
"N30": 1107,
"N40": 1107,
"N50": 1107,
"gc_content": 0,
"longest": 1107,
"mean": 216.1875833243253,
"median": 189.0,
"sequence_count": 27753,
"shortest": 101,
"total_bps": 5999854
},
"Scaffold Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 1107,
"N20": 1107,
"N30": 1107,
"N40": 1107,
"N50": 1107,
"gc_content": 0,
"longest": 1107,
"mean": 216.1875833243253,
"median": 189.0,
"sequence_count": 27753,
"shortest": 101,
"total_bps": 5999854
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa
ok
{
"Contig Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 1107,
"N20": 1107,
"N30": 1107,
"N40": 1107,
"N50": 1107,
"gc_content": 0,
"longest": 1107,
"mean": 216.1875833243253,
"median": 189.0,
"sequence_count": 27753,
"shortest": 101,
"total_bps": 5999854
},
"Scaffold Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 1107,
"N20": 1107,
"N30": 1107,
"N40": 1107,
"N50": 1107,
"gc_content": 0,
"longest": 1107,
"mean": 216.1875833243253,
"median": 189.0,
"sequence_count": 27753,
"shortest": 101,
"total_bps": 5999854
}
}
F: /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
ok
{
"Contig Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 1369,
"N20": 1369,
"N30": 1369,
"N40": 1369,
"N50": 1369,
"gc_content": 0,
"longest": 1369,
"mean": 213.4881373204675,
"median": 187.0,
"sequence_count": 31401,
"shortest": 101,
"total_bps": 6703741
},
"Scaffold Stats": {
"L10": 0,
"L20": 0,
"L30": 0,
"L40": 0,
"L50": 0,
"N10": 1369,
"N20": 1369,
"N30": 1369,
"N40": 1369,
"N50": 1369,
"gc_content": 0,
"longest": 1369,
"mean": 213.4881373204675,
"median": 187.0,
"sequence_count": 31401,
"shortest": 101,
"total_bps": 6703741
}
}
Raw
whole.log
START
cd /home/studentx99/xprusa/cvic2/ws1 ; rm ./wgsim/out* ; rm ./sample/sample.out ; rm ./sample/sample.out
START-wgsim
OUT_PREFIX: out_paired_2000.er_0.5.
cd /home/studentx99/xprusa/cvic2/ws1/wgsim ; ./wgsim -N50000 -1150 -2150 -d2000 -e0.5 ./GCF_000005845.2_ASM584v2_genomic.fna out_paired_2000.er_0.5.1.fq out_paired_2000.er_0.5.2.fq > /dev/null ; head -n5 out_paired_2000.er_0.5.1.fq
[wgsim] seed = 1615923560
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 1 sequences, total length: 4641652
@NC_000913.3_873031_875015_81:0:0_88:0:0_0/1
GGCATGTTTCGGGCTAATTTGCATCAATCGCTCCACAAGTTCAAACCTAGGGACGCTGCCTTTAAGAGAGCTGACCAGCCATCTTGTGTTGTGGAAGCGGCGCTTATGAATGCAGCTGTATTACACAGGGACCAGCCAGTGAGGATGTTA
+
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
@NC_000913.3_2518657_2520578_79:0:0_80:0:0_1/1
OUT_PREFIX: out_paired_2000.er_0.05.
cd /home/studentx99/xprusa/cvic2/ws1/wgsim ; ./wgsim -N50000 -1150 -2150 -d2000 -e0.05 ./GCF_000005845.2_ASM584v2_genomic.fna out_paired_2000.er_0.05.1.fq out_paired_2000.er_0.05.2.fq > /dev/null ; head -n5 out_paired_2000.er_0.05.1.fq
[wgsim] seed = 1615923561
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 1 sequences, total length: 4641652
@NC_000913.3_4469181_4471141_11:0:0_6:0:0_0/1
ATCGACAATGTGCTGGTGTGCGCGAACAGCAACTGTATCATCCATGCCGAACCGGTTTCATCCAGCTTTGCCGTGCGAAAACGGGCCAATGATATCGCGCTCAAATGCCAATACTGTGAAAAAGAGTTTTCGCATAATGTGGTGCTGGCC
+
......................................................................................................................................................
@NC_000913.3_2243654_2245643_6:0:0_6:0:0_1/1
OUT_PREFIX: out_paired_0.er_0.5.
cd /home/studentx99/xprusa/cvic2/ws1/wgsim ; ./wgsim -N50000 -1150 -2150 -d0 -e0.5 ./GCF_000005845.2_ASM584v2_genomic.fna out_paired_0.er_0.5.1.fq out_paired_0.er_0.5.2.fq > /dev/null ; head -n5 out_paired_0.er_0.5.1.fq
[wgsim] seed = 1615923562
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 1 sequences, total length: 4641652
@NC_000913.3_3948237_3948386_66:0:0_73:0:0_0/1
CTGCGTTAAGCGAGGCAGCTACACAGTACTTATGATACTTGCGTGGGTAACTTGATCGAGAGAGAGCAGCAGCAGGCGTGAGTACCACGAATCAGACGCGTCTAAATGGACGAACACTAATAGACAGCCAAAGCTTGTGACACCGGCCTT
+
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
@NC_000913.3_3522390_3522539_69:0:0_65:0:0_1/1
OUT_PREFIX: out_paired_0.er_0.05.
cd /home/studentx99/xprusa/cvic2/ws1/wgsim ; ./wgsim -N50000 -1150 -2150 -d0 -e0.05 ./GCF_000005845.2_ASM584v2_genomic.fna out_paired_0.er_0.05.1.fq out_paired_0.er_0.05.2.fq > /dev/null ; head -n5 out_paired_0.er_0.05.1.fq
[wgsim] seed = 1615923563
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 1 sequences, total length: 4641652
@NC_000913.3_1557314_1557463_11:0:0_10:0:0_0/1
GGGGCTGACCTATGTGCTGATTTCACACAATGTCTGGGTGATCCGTCATATGAGCGCTCGGGTGGCGGTGATGAATCTCGTGCAGATTGTAGAAGAGGTCGACGCGCAGCAGGTGCTGACGGCACCTGCACATCCATACACCCTATTATT
+
......................................................................................................................................................
@NC_000913.3_3371249_3371398_3:0:0_7:0:0_1/1
START-sample
1
cd /home/studentx99/xprusa/cvic2/ws1/sample ; ./sample --sample-size=50000 --lines-per-offset=4 /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq > /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_1.out ; head -n5 /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_1.out
@NC_000913.3_4469181_4471141_11:0:0_6:0:0_0/1
ATCGACAATGTGCTGGTGTGCGCGAACAGCAACTGTATCATCCATGCCGAACCGGTTTCATCCAGCTTTGCCGTGCGAAAACGGGCCAATGATATCGCGCTCAAATGCCAATACTGTGAAAAAGAGTTTTCGCATAATGTGGTGCTGGCC
+
......................................................................................................................................................
@NC_000913.3_2243654_2245643_6:0:0_6:0:0_1/1
8
cd /home/studentx99/xprusa/cvic2/ws1/sample ; ./sample --sample-size=400000 --lines-per-offset=4 /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq > /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_8.out ; head -n5 /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_8.out
@NC_000913.3_4469181_4471141_11:0:0_6:0:0_0/1
ATCGACAATGTGCTGGTGTGCGCGAACAGCAACTGTATCATCCATGCCGAACCGGTTTCATCCAGCTTTGCCGTGCGAAAACGGGCCAATGATATCGCGCTCAAATGCCAATACTGTGAAAAAGAGTTTTCGCATAATGTGGTGCTGGCC
+
......................................................................................................................................................
@NC_000913.3_2243654_2245643_6:0:0_6:0:0_1/1
START-velvet
START-velveth
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velveth ./ 31 -fastq /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_1.out /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq ;
[0.000000] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_1.out;
[0.440097] 50000 sequences found
[0.440200] Done
[0.440269] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq;
[0.625371] 50000 sequences found
[0.625454] Done
[0.669642] Reading read set file .//Sequences;
[0.685136] 100000 sequences found
[0.766607] Done
[0.766710] 100000 sequences in total.
[0.767617] Writing into roadmap file .//Roadmaps...
[0.898794] Inputting sequences...
[0.898888] Inputting sequence 0 / 100000
[4.218123] === Sequences loaded in 3.319331 s
[4.218530] Done inputting sequences
[4.218542] Destroying splay table
[4.254585] Splay table destroyed
START-velvetg
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500
[0.000000] Reading roadmap file .//Roadmaps
[0.287182] 100000 roadmaps read
[0.287373] Creating insertion markers
[0.307650] Ordering insertion markers
[0.322989] Counting preNodes
[0.333157] 96730 preNodes counted, creating them now
[0.792826] Adjusting marker info...
[0.826599] Connecting preNodes
[0.867471] Cleaning up memory
[0.867672] Done creating preGraph
[0.867713] Concatenation...
[0.876983] Renumbering preNodes
[0.877044] Initial preNode count 96730
[0.879755] Destroyed 4796 preNodes
[0.879797] Concatenation over!
[0.879827] Clipping short tips off preGraph
[0.896325] Concatenation...
[0.902490] Renumbering preNodes
[0.902557] Initial preNode count 91934
[0.905153] Destroyed 3720 preNodes
[0.905199] Concatenation over!
[0.905229] 1902 tips cut off
[0.905255] 88214 nodes left
[0.905321] Writing into pregraph file .//PreGraph...
[1.584017] Reading read set file .//Sequences;
[1.616718] 100000 sequences found
[1.727078] Done
[1.952586] Reading pre-graph file .//PreGraph
[1.952746] Graph has 88214 nodes and 100000 sequences
[2.176541] Scanning pre-graph file .//PreGraph for k-mers
[2.220447] 5779746 kmers found
[2.650255] Sorting kmer occurence table ...
[5.211573] Sorting done.
[5.211584] Computing acceleration table...
[5.350070] Computing offsets...
[5.395969] Ghost Threading through reads 0 / 100000
[9.150790] === Ghost-Threaded in 3.754822 s
[9.150804] Threading through reads 0 / 100000
[13.565077] === Threaded in 4.414273 s
[13.578852] Correcting graph with cutoff 0.200000
[13.582958] Determining eligible starting points
[13.645850] Done listing starting nodes
[13.646181] Initializing todo lists
[13.654784] Done with initilization
[13.654869] Activating arc lookup table
[13.670659] Done activating arc lookup table
[13.732865] 10000 / 88214 nodes visited
[13.747410] 20000 / 88214 nodes visited
[13.777200] 30000 / 88214 nodes visited
[13.805482] 40000 / 88214 nodes visited
[13.816545] 50000 / 88214 nodes visited
[13.825304] 60000 / 88214 nodes visited
[13.828034] 70000 / 88214 nodes visited
[13.830324] 80000 / 88214 nodes visited
[13.832432] Concatenation...
[13.835529] Renumbering nodes
[13.835599] Initial node count 88214
[13.837206] Removed 2495 null nodes
[13.837252] Concatenation over!
[13.837282] Clipping short tips off graph, drastic
[13.925475] Concatenation...
[13.983389] Renumbering nodes
[13.983480] Initial node count 85719
[13.990371] Removed 42493 null nodes
[13.990463] Concatenation over!
[13.990494] 43226 nodes left
[13.990565] Writing into graph file .//Graph2...
[14.815533] Measuring median coverage depth...
[14.828199] Median coverage depth = 2.000000
[14.828375] Removing contigs with coverage < 1.000000...
[14.829438] Concatenation...
[14.830682] Renumbering nodes
[14.830720] Initial node count 43226
[14.830815] Removed 0 null nodes
[14.830847] Concatenation over!
[14.831966] Concatenation...
[14.833121] Renumbering nodes
[14.833158] Initial node count 43226
[14.833252] Removed 0 null nodes
[14.833283] Concatenation over!
[14.833313] Clipping short tips off graph, drastic
[14.835636] Concatenation...
[14.836694] Renumbering nodes
[14.836731] Initial node count 43226
[14.836825] Removed 0 null nodes
[14.836857] Concatenation over!
[14.836885] 43226 nodes left
[14.836915] Read coherency...
[14.837882] Identifying unique nodes
[14.839014] Done, 41550 unique nodes counted
[14.839055] Trimming read tips
[14.840851] Renumbering nodes
[14.840891] Initial node count 43226
[14.840985] Removed 0 null nodes
[14.841018] Confronted to 0 multiple hits and 0 null over 0
[14.841048] Read coherency over!
[14.841580] Starting pebble resolution...
[14.843248] Computing read to node mapping array sizes
[14.848815] Computing read to node mappings
[14.855716] Estimating library insert lengths...
[14.856263] Done
[14.856325] Computing direct node to node mappings
[14.856510] Scaffolding node -40000
[14.857123] Scaffolding node -30000
[14.857986] Scaffolding node -20000
[14.859019] Scaffolding node -10000
[14.860254] Scaffolding node 0
[14.861959] Scaffolding node 10000
[14.863565] Scaffolding node 20000
[14.865000] Scaffolding node 30000
[14.866152] Scaffolding node 40000
[14.866884] === Nodes Scaffolded in 0.010525 s
[14.870820] Preparing to correct graph with cutoff 0.200000
[14.895762] Cleaning memory
[14.895886] Deactivating local correction settings
[14.896465] Pebble done.
[14.896503] Concatenation...
[14.897784] Renumbering nodes
[14.897823] Initial node count 43226
[14.898610] Removed 4 null nodes
[14.899098] Concatenation over!
[14.899135] Removing reference contigs with coverage < 1.000000...
[14.900821] Concatenation...
[14.901962] Renumbering nodes
[14.901999] Initial node count 43222
[14.902104] Removed 0 null nodes
[14.902524] Concatenation over!
[14.903108] Writing contigs into .//contigs.fa...
[15.739017] Writing into stats file .//stats.txt...
[15.887018] Writing into graph file .//LastGraph...
[16.501038] Estimated Coverage = 2.000000
[16.501052] Estimated Coverage cutoff = 1.000000
Final graph has 43222 nodes and n50 of 120, max 469, total 5013597, using 98674/100000 reads
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_1.cv_31.fa
START-velveth
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velveth ./ 31 -fastq /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_8.out /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq ;
[0.000000] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_8.out;
[0.261697] 50000 sequences found
[0.261778] Done
[0.261831] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq;
[0.466871] 50000 sequences found
[0.466948] Done
[0.510703] Reading read set file .//Sequences;
[0.541672] 100000 sequences found
[0.641308] Done
[0.641398] 100000 sequences in total.
[0.641794] Writing into roadmap file .//Roadmaps...
[0.881719] Inputting sequences...
[0.881818] Inputting sequence 0 / 100000
[3.969397] === Sequences loaded in 3.087680 s
[3.969853] Done inputting sequences
[3.969901] Destroying splay table
[3.985291] Splay table destroyed
START-velvetg
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500
[0.000000] Reading roadmap file .//Roadmaps
[0.217290] 100000 roadmaps read
[0.217465] Creating insertion markers
[0.221626] Ordering insertion markers
[0.229582] Counting preNodes
[0.233194] 96730 preNodes counted, creating them now
[0.579125] Adjusting marker info...
[0.581485] Connecting preNodes
[0.591311] Cleaning up memory
[0.591518] Done creating preGraph
[0.591564] Concatenation...
[0.600512] Renumbering preNodes
[0.600582] Initial preNode count 96730
[0.603340] Destroyed 4796 preNodes
[0.603388] Concatenation over!
[0.603418] Clipping short tips off preGraph
[0.620638] Concatenation...
[0.626593] Renumbering preNodes
[0.626641] Initial preNode count 91934
[0.629236] Destroyed 3720 preNodes
[0.629282] Concatenation over!
[0.629311] 1902 tips cut off
[0.629347] 88214 nodes left
[0.629409] Writing into pregraph file .//PreGraph...
[1.378160] Reading read set file .//Sequences;
[1.413577] 100000 sequences found
[1.567391] Done
[1.883894] Reading pre-graph file .//PreGraph
[1.884042] Graph has 88214 nodes and 100000 sequences
[2.116746] Scanning pre-graph file .//PreGraph for k-mers
[2.194496] 5779746 kmers found
[2.605177] Sorting kmer occurence table ...
[5.248313] Sorting done.
[5.248410] Computing acceleration table...
[5.385114] Computing offsets...
[5.415092] Ghost Threading through reads 0 / 100000
[9.342500] === Ghost-Threaded in 3.927409 s
[9.342590] Threading through reads 0 / 100000
[2212.198413] Concatenation...
[2215.089854] Renumbering nodes
[2215.089858] Initial node count 22916387
[2215.592542] Removed 9694497 null nodes
[2215.592546] Concatenation over!
[2215.592547] Clipping short tips off graph, drastic
[2224.597334] Concatenation...
[2234.066601] Renumbering nodes
[2234.066605] Initial node count 13221890
[2234.380979] Removed 5669337 null nodes
[2234.380983] Concatenation over!
[2234.380983] 7552553 nodes left
[2234.480809] Writing into graph file .//Graph2...
[2375.368861] Measuring median coverage depth...
[2382.707168] Median coverage depth = 2.000000
[2382.707196] Removing contigs with coverage < 1.000000...
[2383.116732] Concatenation...
[2384.991629] Renumbering nodes
[2384.991633] Initial node count 7552553
[2385.003084] Removed 0 null nodes
[2385.003086] Concatenation over!
[2385.472170] Concatenation...
[2386.975664] Renumbering nodes
[2386.975668] Initial node count 7552553
[2386.987207] Removed 0 null nodes
[2386.987209] Concatenation over!
[2386.987210] Clipping short tips off graph, drastic
[2387.584559] Concatenation...
[2389.283135] Renumbering nodes
[2389.283138] Initial node count 7552553
[2389.294620] Removed 0 null nodes
[2389.294622] Concatenation over!
[2389.294622] 7552553 nodes left
[2389.294627] Read coherency...
[2389.634698] Identifying unique nodes
[2389.900878] Done, 1437377 unique nodes counted
[2389.900880] Trimming read tips
[2390.975490] Renumbering nodes
[2390.975492] Initial node count 7552553
[2390.986991] Removed 0 null nodes
[2390.986993] Confronted to 0 multiple hits and 0 null over 0
[2390.986994] Read coherency over!
[2391.070407] Starting pebble resolution...
[2391.472834] Computing read to node mapping array sizes
[2399.497321] Computing read to node mappings
[2430.004360] Estimating library insert lengths...
[2430.073044] Done
[2430.084721] Computing direct node to node mappings
[2430.084911] Scaffolding node -7550000
[2430.085611] Scaffolding node -7540000
[2430.086282] Scaffolding node -7530000
[2430.086943] Scaffolding node -7520000
[2430.087599] Scaffolding node -7510000
[2430.088253] Scaffolding node -7500000
[2430.088905] Scaffolding node -7490000
[2430.089555] Scaffolding node -7480000
[2430.090215] Scaffolding node -7470000
[2430.090861] Scaffolding node -7460000
[2430.091519] Scaffolding node -7450000
[2430.092159] Scaffolding node -7440000
[2430.092808] Scaffolding node -7430000
[2430.093454] Scaffolding node -7420000
[2430.094089] Scaffolding node -7410000
[2430.107724] Scaffolding node -7400000
[2430.108349] Scaffolding node -7390000
[2430.108970] Scaffolding node -7380000
[2430.109586] Scaffolding node -7370000
[2430.110195] Scaffolding node -7360000
[2430.110796] Scaffolding node -7350000
[2430.111413] Scaffolding node -7340000
[2430.112020] Scaffolding node -7330000
[2430.112631] Scaffolding node -7320000
[2430.113255] Scaffolding node -7310000
[2430.113923] Scaffolding node -7300000
[2430.114561] Scaffolding node -7290000
[2430.115201] Scaffolding node -7280000
[2430.115837] Scaffolding node -7270000
[2430.116476] Scaffolding node -7260000
[2430.117114] Scaffolding node -7250000
[2430.117743] Scaffolding node -7240000
[2430.118372] Scaffolding node -7230000
[2430.119004] Scaffolding node -7220000
[2430.119647] Scaffolding node -7210000
[2430.120312] Scaffolding node -7200000
[2430.120945] Scaffolding node -7190000
[2430.121584] Scaffolding node -7180000
[2430.122220] Scaffolding node -7170000
[2430.122856] Scaffolding node -7160000
[2430.123491] Scaffolding node -7150000
[2430.124124] Scaffolding node -7140000
[2430.124762] Scaffolding node -7130000
[2430.125403] Scaffolding node -7120000
[2430.126035] Scaffolding node -7110000
[2430.126670] Scaffolding node -7100000
[2430.127313] Scaffolding node -7090000
[2430.127942] Scaffolding node -7080000
[2430.128576] Scaffolding node -7070000
[2430.129197] Scaffolding node -7060000
[2430.129826] Scaffolding node -7050000
[2430.130455] Scaffolding node -7040000
[2430.131088] Scaffolding node -7030000
[2430.131712] Scaffolding node -7020000
[2430.132343] Scaffolding node -7010000
[2430.133024] Scaffolding node -7000000
[2430.133814] Scaffolding node -6990000
[2430.134446] Scaffolding node -6980000
[2430.135074] Scaffolding node -6970000
[2430.135696] Scaffolding node -6960000
[2430.136328] Scaffolding node -6950000
[2430.136949] Scaffolding node -6940000
[2430.137577] Scaffolding node -6930000
[2430.138197] Scaffolding node -6920000
[2430.138823] Scaffolding node -6910000
[2430.139444] Scaffolding node -6900000
[2430.140063] Scaffolding node -6890000
[2430.140695] Scaffolding node -6880000
[2430.141331] Scaffolding node -6870000
[2430.141947] Scaffolding node -6860000
[2430.142569] Scaffolding node -6850000
[2430.143203] Scaffolding node -6840000
[2430.143834] Scaffolding node -6830000
[2430.144521] Scaffolding node -6820000
[2430.145160] Scaffolding node -6810000
[2430.145784] Scaffolding node -6800000
[2430.146407] Scaffolding node -6790000
[2430.147039] Scaffolding node -6780000
[2430.147661] Scaffolding node -6770000
[2430.148312] Scaffolding node -6760000
[2430.148945] Scaffolding node -6750000
[2430.149586] Scaffolding node -6740000
[2430.150212] Scaffolding node -6730000
[2430.150832] Scaffolding node -6720000
[2430.151451] Scaffolding node -6710000
[2430.152083] Scaffolding node -6700000
[2430.152709] Scaffolding node -6690000
[2430.153337] Scaffolding node -6680000
[2430.153967] Scaffolding node -6670000
[2430.154590] Scaffolding node -6660000
[2430.155215] Scaffolding node -6650000
[2430.155839] Scaffolding node -6640000
[2430.163915] Scaffolding node -6630000
[2430.164539] Scaffolding node -6620000
[2430.165169] Scaffolding node -6610000
[2430.165794] Scaffolding node -6600000
[2430.166422] Scaffolding node -6590000
[2430.167042] Scaffolding node -6580000
[2430.167662] Scaffolding node -6570000
[2430.168291] Scaffolding node -6560000
[2430.168903] Scaffolding node -6550000
[2430.169523] Scaffolding node -6540000
[2430.170137] Scaffolding node -6530000
[2430.170754] Scaffolding node -6520000
[2430.171371] Scaffolding node -6510000
[2430.171991] Scaffolding node -6500000
[2430.185323] Scaffolding node -6490000
[2430.185943] Scaffolding node -6480000
[2430.186567] Scaffolding node -6470000
[2430.187179] Scaffolding node -6460000
[2430.187794] Scaffolding node -6450000
[2430.188411] Scaffolding node -6440000
[2430.189028] Scaffolding node -6430000
[2430.189650] Scaffolding node -6420000
[2430.190290] Scaffolding node -6410000
[2430.190933] Scaffolding node -6400000
[2430.191575] Scaffolding node -6390000
[2430.202384] Scaffolding node -6380000
[2430.203019] Scaffolding node -6370000
[2430.203641] Scaffolding node -6360000
[2430.204259] Scaffolding node -6350000
[2430.204879] Scaffolding node -6340000
[2430.205515] Scaffolding node -6330000
[2430.206140] Scaffolding node -6320000
[2430.206779] Scaffolding node -6310000
[2430.207416] Scaffolding node -6300000
[2430.208044] Scaffolding node -6290000
[2430.208675] Scaffolding node -6280000
[2430.209319] Scaffolding node -6270000
[2430.209933] Scaffolding node -6260000
[2430.211550] Scaffolding node -6250000
[2430.212168] Scaffolding node -6240000
[2430.212796] Scaffolding node -6230000
[2430.217046] Scaffolding node -6220000
[2430.217739] Scaffolding node -6210000
[2430.218327] Scaffolding node -6200000
[2430.218910] Scaffolding node -6190000
[2430.219491] Scaffolding node -6180000
[2430.220073] Scaffolding node -6170000
[2430.220683] Scaffolding node -6160000
[2430.243025] Scaffolding node -6150000
[2430.243603] Scaffolding node -6140000
[2430.244182] Scaffolding node -6130000
[2430.244738] Scaffolding node -6120000
[2430.245306] Scaffolding node -6110000
[2430.245869] Scaffolding node -6100000
[2430.246454] Scaffolding node -6090000
[2430.247013] Scaffolding node -6080000
[2430.247590] Scaffolding node -6070000
[2430.248162] Scaffolding node -6060000
[2430.248738] Scaffolding node -6050000
[2430.249319] Scaffolding node -6040000
[2430.249886] Scaffolding node -6030000
[2430.250451] Scaffolding node -6020000
[2430.251024] Scaffolding node -6010000
[2430.251583] Scaffolding node -6000000
[2430.252140] Scaffolding node -5990000
[2430.252693] Scaffolding node -5980000
[2430.253356] Scaffolding node -5970000
[2430.253935] Scaffolding node -5960000
[2430.257956] Scaffolding node -5950000
[2430.258544] Scaffolding node -5940000
[2430.259128] Scaffolding node -5930000
[2430.259706] Scaffolding node -5920000
[2430.260281] Scaffolding node -5910000
[2430.260850] Scaffolding node -5900000
[2430.261440] Scaffolding node -5890000
[2430.262020] Scaffolding node -5880000
[2430.262604] Scaffolding node -5870000
[2430.263185] Scaffolding node -5860000
[2430.263804] Scaffolding node -5850000
[2430.264401] Scaffolding node -5840000
[2430.264989] Scaffolding node -5830000
[2430.265560] Scaffolding node -5820000
[2430.266126] Scaffolding node -5810000
[2430.266693] Scaffolding node -5800000
[2430.267266] Scaffolding node -5790000
[2430.267840] Scaffolding node -5780000
[2430.268413] Scaffolding node -5770000
[2430.268980] Scaffolding node -5760000
[2430.269548] Scaffolding node -5750000
[2430.277678] Scaffolding node -5740000
[2430.278282] Scaffolding node -5730000
[2430.278894] Scaffolding node -5720000
[2430.279513] Scaffolding node -5710000
[2430.280117] Scaffolding node -5700000
[2430.280727] Scaffolding node -5690000
[2430.281335] Scaffolding node -5680000
[2430.281953] Scaffolding node -5670000
[2430.282559] Scaffolding node -5660000
[2430.283160] Scaffolding node -5650000
[2430.283783] Scaffolding node -5640000
[2430.284399] Scaffolding node -5630000
[2430.285012] Scaffolding node -5620000
[2430.293636] Scaffolding node -5610000
[2430.294248] Scaffolding node -5600000
[2430.294857] Scaffolding node -5590000
[2430.295464] Scaffolding node -5580000
[2430.296073] Scaffolding node -5570000
[2430.296685] Scaffolding node -5560000
[2430.297300] Scaffolding node -5550000
[2430.297904] Scaffolding node -5540000
[2430.298519] Scaffolding node -5530000
[2430.299110] Scaffolding node -5520000
[2430.299698] Scaffolding node -5510000
[2430.300283] Scaffolding node -5500000
[2430.300874] Scaffolding node -5490000
[2430.309474] Scaffolding node -5480000
[2430.310067] Scaffolding node -5470000
[2430.310654] Scaffolding node -5460000
[2430.311242] Scaffolding node -5450000
[2430.311831] Scaffolding node -5440000
[2430.312429] Scaffolding node -5430000
[2430.313039] Scaffolding node -5420000
[2430.313646] Scaffolding node -5410000
[2430.314247] Scaffolding node -5400000
[2430.314848] Scaffolding node -5390000
[2430.315452] Scaffolding node -5380000
[2430.316052] Scaffolding node -5370000
[2430.316651] Scaffolding node -5360000
[2430.325302] Scaffolding node -5350000
[2430.325904] Scaffolding node -5340000
[2430.326509] Scaffolding node -5330000
[2430.327117] Scaffolding node -5320000
[2430.327719] Scaffolding node -5310000
[2430.328325] Scaffolding node -5300000
[2430.328923] Scaffolding node -5290000
[2430.329528] Scaffolding node -5280000
[2430.330160] Scaffolding node -5270000
[2430.330754] Scaffolding node -5260000
[2430.331357] Scaffolding node -5250000
[2430.331960] Scaffolding node -5240000
[2430.332560] Scaffolding node -5230000
[2430.341191] Scaffolding node -5220000
[2430.341791] Scaffolding node -5210000
[2430.342392] Scaffolding node -5200000
[2430.342996] Scaffolding node -5190000
[2430.343598] Scaffolding node -5180000
[2430.344198] Scaffolding node -5170000
[2430.344802] Scaffolding node -5160000
[2430.353154] Scaffolding node -5150000
[2430.353726] Scaffolding node -5140000
[2430.354296] Scaffolding node -5130000
[2430.354863] Scaffolding node -5120000
[2430.355695] Scaffolding node -5110000
[2430.356265] Scaffolding node -5100000
[2430.356827] Scaffolding node -5090000
[2430.357387] Scaffolding node -5080000
[2430.358675] Scaffolding node -5070000
[2430.359239] Scaffolding node -5060000
[2430.359801] Scaffolding node -5050000
[2430.360362] Scaffolding node -5040000
[2430.360931] Scaffolding node -5030000
[2430.361509] Scaffolding node -5020000
[2430.362064] Scaffolding node -5010000
[2430.362604] Scaffolding node -5000000
[2430.363159] Scaffolding node -4990000
[2430.363716] Scaffolding node -4980000
[2430.364268] Scaffolding node -4970000
[2430.366491] Scaffolding node -4960000
[2430.368623] Scaffolding node -4950000
[2430.369284] Scaffolding node -4940000
[2430.369828] Scaffolding node -4930000
[2430.370373] Scaffolding node -4920000
[2430.370945] Scaffolding node -4910000
[2430.371497] Scaffolding node -4900000
[2430.372042] Scaffolding node -4890000
[2430.372589] Scaffolding node -4880000
[2430.373149] Scaffolding node -4870000
[2430.373692] Scaffolding node -4860000
[2430.374234] Scaffolding node -4850000
[2430.374787] Scaffolding node -4840000
[2430.375333] Scaffolding node -4830000
[2430.375877] Scaffolding node -4820000
[2430.376416] Scaffolding node -4810000
[2430.376960] Scaffolding node -4800000
[2430.377515] Scaffolding node -4790000
[2430.378072] Scaffolding node -4780000
[2430.378635] Scaffolding node -4770000
[2430.379192] Scaffolding node -4760000
[2430.379749] Scaffolding node -4750000
[2430.380305] Scaffolding node -4740000
[2430.380863] Scaffolding node -4730000
[2430.381442] Scaffolding node -4720000
[2430.383629] Scaffolding node -4710000
[2430.384191] Scaffolding node -4700000
[2430.384754] Scaffolding node -4690000
[2430.385323] Scaffolding node -4680000
[2430.390149] Scaffolding node -4670000
[2430.391420] Scaffolding node -4660000
[2430.391986] Scaffolding node -4650000
[2430.392546] Scaffolding node -4640000
[2430.393132] Scaffolding node -4630000
[2430.393689] Scaffolding node -4620000
[2430.394246] Scaffolding node -4610000
[2430.394810] Scaffolding node -4600000
[2430.395367] Scaffolding node -4590000
[2430.395924] Scaffolding node -4580000
[2430.396488] Scaffolding node -4570000
[2430.397077] Scaffolding node -4560000
[2430.397638] Scaffolding node -4550000
[2430.398198] Scaffolding node -4540000
[2430.398749] Scaffolding node -4530000
[2430.399301] Scaffolding node -4520000
[2430.399860] Scaffolding node -4510000
[2430.400436] Scaffolding node -4500000
[2430.400986] Scaffolding node -4490000
[2430.401568] Scaffolding node -4480000
[2430.402122] Scaffolding node -4470000
[2430.402669] Scaffolding node -4460000
[2430.403226] Scaffolding node -4450000
[2430.403799] Scaffolding node -4440000
[2430.404391] Scaffolding node -4430000
[2430.404946] Scaffolding node -4420000
[2430.406311] Scaffolding node -4410000
[2430.406869] Scaffolding node -4400000
[2430.407491] Scaffolding node -4390000
[2430.408046] Scaffolding node -4380000
[2430.408601] Scaffolding node -4370000
[2430.409172] Scaffolding node -4360000
[2430.409801] Scaffolding node -4350000
[2430.410353] Scaffolding node -4340000
[2430.410908] Scaffolding node -4330000
[2430.411465] Scaffolding node -4320000
[2430.412029] Scaffolding node -4310000
[2430.412591] Scaffolding node -4300000
[2430.413426] Scaffolding node -4290000
[2430.413984] Scaffolding node -4280000
[2430.414553] Scaffolding node -4270000
[2430.415110] Scaffolding node -4260000
[2430.415716] Scaffolding node -4250000
[2430.416285] Scaffolding node -4240000
[2430.416841] Scaffolding node -4230000
[2430.417437] Scaffolding node -4220000
[2430.417986] Scaffolding node -4210000
[2430.418541] Scaffolding node -4200000
[2430.419101] Scaffolding node -4190000
[2430.419663] Scaffolding node -4180000
[2430.420222] Scaffolding node -4170000
[2430.420783] Scaffolding node -4160000
[2430.421335] Scaffolding node -4150000
[2430.421896] Scaffolding node -4140000
[2430.422452] Scaffolding node -4130000
[2430.423034] Scaffolding node -4120000
[2430.423594] Scaffolding node -4110000
[2430.424148] Scaffolding node -4100000
[2430.424715] Scaffolding node -4090000
[2430.425276] Scaffolding node -4080000
[2430.425825] Scaffolding node -4070000
[2430.426369] Scaffolding node -4060000
[2430.426906] Scaffolding node -4050000
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[2430.427984] Scaffolding node -4030000
[2430.428528] Scaffolding node -4020000
[2430.429073] Scaffolding node -4010000
[2430.429617] Scaffolding node -4000000
[2430.430159] Scaffolding node -3990000
[2430.430712] Scaffolding node -3980000
[2430.431249] Scaffolding node -3970000
[2430.431783] Scaffolding node -3960000
[2430.432316] Scaffolding node -3950000
[2430.432858] Scaffolding node -3940000
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[2430.436609] Scaffolding node -3920000
[2430.437155] Scaffolding node -3910000
[2430.437698] Scaffolding node -3900000
[2430.438245] Scaffolding node -3890000
[2430.438783] Scaffolding node -3880000
[2430.439329] Scaffolding node -3870000
[2430.439885] Scaffolding node -3860000
[2430.440433] Scaffolding node -3850000
[2430.441033] Scaffolding node -3840000
[2430.441581] Scaffolding node -3830000
[2430.442124] Scaffolding node -3820000
[2430.442678] Scaffolding node -3810000
[2430.443221] Scaffolding node -3800000
[2430.443767] Scaffolding node -3790000
[2430.444314] Scaffolding node -3780000
[2430.444856] Scaffolding node -3770000
[2430.445411] Scaffolding node -3760000
[2430.445949] Scaffolding node -3750000
[2430.446487] Scaffolding node -3740000
[2430.447022] Scaffolding node -3730000
[2430.447562] Scaffolding node -3720000
[2430.448102] Scaffolding node -3710000
[2430.448671] Scaffolding node -3700000
[2430.449235] Scaffolding node -3690000
[2430.449789] Scaffolding node -3680000
[2430.450324] Scaffolding node -3670000
[2430.450871] Scaffolding node -3660000
[2430.451404] Scaffolding node -3650000
[2430.451952] Scaffolding node -3640000
[2430.452497] Scaffolding node -3630000
[2430.453024] Scaffolding node -3620000
[2430.453564] Scaffolding node -3610000
[2430.454120] Scaffolding node -3600000
[2430.454654] Scaffolding node -3590000
[2430.455191] Scaffolding node -3580000
[2430.455747] Scaffolding node -3570000
[2430.456270] Scaffolding node -3560000
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[2430.457989] Scaffolding node -3540000
[2430.458529] Scaffolding node -3530000
[2430.459056] Scaffolding node -3520000
[2430.459588] Scaffolding node -3510000
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[2430.460680] Scaffolding node -3490000
[2430.461271] Scaffolding node -3480000
[2430.461797] Scaffolding node -3470000
[2430.462323] Scaffolding node -3460000
[2430.462847] Scaffolding node -3450000
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[2430.463897] Scaffolding node -3430000
[2430.464426] Scaffolding node -3420000
[2430.464950] Scaffolding node -3410000
[2430.465474] Scaffolding node -3400000
[2430.465991] Scaffolding node -3390000
[2430.466518] Scaffolding node -3380000
[2430.467039] Scaffolding node -3370000
[2430.468998] Scaffolding node -3360000
[2430.469531] Scaffolding node -3350000
[2430.470058] Scaffolding node -3340000
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[2430.471094] Scaffolding node -3320000
[2430.471610] Scaffolding node -3310000
[2430.472131] Scaffolding node -3300000
[2430.472639] Scaffolding node -3290000
[2430.473267] Scaffolding node -3280000
[2430.473783] Scaffolding node -3270000
[2430.474292] Scaffolding node -3260000
[2430.474807] Scaffolding node -3250000
[2430.475317] Scaffolding node -3240000
[2430.475816] Scaffolding node -3230000
[2430.476313] Scaffolding node -3220000
[2430.476839] Scaffolding node -3210000
[2430.477352] Scaffolding node -3200000
[2430.477856] Scaffolding node -3190000
[2430.478359] Scaffolding node -3180000
[2430.478865] Scaffolding node -3170000
[2430.479369] Scaffolding node -3160000
[2430.479870] Scaffolding node -3150000
[2430.480373] Scaffolding node -3140000
[2430.480917] Scaffolding node -3130000
[2430.481463] Scaffolding node -3120000
[2430.481976] Scaffolding node -3110000
[2430.482477] Scaffolding node -3100000
[2430.482990] Scaffolding node -3090000
[2430.483489] Scaffolding node -3080000
[2430.483996] Scaffolding node -3070000
[2430.484492] Scaffolding node -3060000
[2430.484997] Scaffolding node -3050000
[2430.485499] Scaffolding node -3040000
[2430.485990] Scaffolding node -3030000
[2430.486478] Scaffolding node -3020000
[2430.486959] Scaffolding node -3010000
[2430.487452] Scaffolding node -3000000
[2430.487967] Scaffolding node -2990000
[2430.488442] Scaffolding node -2980000
[2430.488926] Scaffolding node -2970000
[2430.489416] Scaffolding node -2960000
[2430.489893] Scaffolding node -2950000
[2430.490372] Scaffolding node -2940000
[2430.490852] Scaffolding node -2930000
[2430.491342] Scaffolding node -2920000
[2430.491818] Scaffolding node -2910000
[2430.494901] Scaffolding node -2900000
[2430.495373] Scaffolding node -2890000
[2430.495855] Scaffolding node -2880000
[2430.496324] Scaffolding node -2870000
[2430.496790] Scaffolding node -2860000
[2430.497260] Scaffolding node -2850000
[2430.497771] Scaffolding node -2840000
[2430.498243] Scaffolding node -2830000
[2430.498729] Scaffolding node -2820000
[2430.499193] Scaffolding node -2810000
[2430.499665] Scaffolding node -2800000
[2430.500138] Scaffolding node -2790000
[2430.500606] Scaffolding node -2780000
[2430.501071] Scaffolding node -2770000
[2430.501552] Scaffolding node -2760000
[2430.502035] Scaffolding node -2750000
[2430.502519] Scaffolding node -2740000
[2430.502995] Scaffolding node -2730000
[2430.503457] Scaffolding node -2720000
[2430.503929] Scaffolding node -2710000
[2430.504499] Scaffolding node -2700000
[2430.504978] Scaffolding node -2690000
[2430.505447] Scaffolding node -2680000
[2430.505909] Scaffolding node -2670000
[2430.506377] Scaffolding node -2660000
[2430.506840] Scaffolding node -2650000
[2430.507316] Scaffolding node -2640000
[2430.507788] Scaffolding node -2630000
[2430.508257] Scaffolding node -2620000
[2430.508718] Scaffolding node -2610000
[2430.509172] Scaffolding node -2600000
[2430.509627] Scaffolding node -2590000
[2430.510093] Scaffolding node -2580000
[2430.510554] Scaffolding node -2570000
[2430.511023] Scaffolding node -2560000
[2430.511480] Scaffolding node -2550000
[2430.511934] Scaffolding node -2540000
[2430.512380] Scaffolding node -2530000
[2430.512916] Scaffolding node -2520000
[2430.513371] Scaffolding node -2510000
[2430.513824] Scaffolding node -2500000
[2430.514285] Scaffolding node -2490000
[2430.514733] Scaffolding node -2480000
[2430.515173] Scaffolding node -2470000
[2430.515615] Scaffolding node -2460000
[2430.516061] Scaffolding node -2450000
[2430.516532] Scaffolding node -2440000
[2430.517010] Scaffolding node -2430000
[2430.517459] Scaffolding node -2420000
[2430.517903] Scaffolding node -2410000
[2430.518343] Scaffolding node -2400000
[2430.518780] Scaffolding node -2390000
[2430.519247] Scaffolding node -2380000
[2430.519684] Scaffolding node -2370000
[2430.520118] Scaffolding node -2360000
[2430.520556] Scaffolding node -2350000
[2430.520984] Scaffolding node -2340000
[2430.521421] Scaffolding node -2330000
[2430.521851] Scaffolding node -2320000
[2430.522282] Scaffolding node -2310000
[2430.522716] Scaffolding node -2300000
[2430.523150] Scaffolding node -2290000
[2430.523572] Scaffolding node -2280000
[2430.524002] Scaffolding node -2270000
[2430.524431] Scaffolding node -2260000
[2430.524865] Scaffolding node -2250000
[2430.525302] Scaffolding node -2240000
[2430.525729] Scaffolding node -2230000
[2430.526154] Scaffolding node -2220000
[2430.526576] Scaffolding node -2210000
[2430.527011] Scaffolding node -2200000
[2430.527816] Scaffolding node -2190000
[2430.528242] Scaffolding node -2180000
[2430.528661] Scaffolding node -2170000
[2430.529085] Scaffolding node -2160000
[2430.529514] Scaffolding node -2150000
[2430.530044] Scaffolding node -2140000
[2430.530495] Scaffolding node -2130000
[2430.530948] Scaffolding node -2120000
[2430.531373] Scaffolding node -2110000
[2430.531795] Scaffolding node -2100000
[2430.532238] Scaffolding node -2090000
[2430.532652] Scaffolding node -2080000
[2430.533107] Scaffolding node -2070000
[2430.533520] Scaffolding node -2060000
[2430.533944] Scaffolding node -2050000
[2430.534357] Scaffolding node -2040000
[2430.534777] Scaffolding node -2030000
[2430.535190] Scaffolding node -2020000
[2430.535605] Scaffolding node -2010000
[2430.536019] Scaffolding node -2000000
[2430.536436] Scaffolding node -1990000
[2430.536856] Scaffolding node -1980000
[2430.538710] Scaffolding node -1970000
[2430.539125] Scaffolding node -1960000
[2430.539541] Scaffolding node -1950000
[2430.539954] Scaffolding node -1940000
[2430.540373] Scaffolding node -1930000
[2430.540773] Scaffolding node -1920000
[2430.541216] Scaffolding node -1910000
[2430.541621] Scaffolding node -1900000
[2430.542028] Scaffolding node -1890000
[2430.542436] Scaffolding node -1880000
[2430.543290] Scaffolding node -1870000
[2430.543729] Scaffolding node -1860000
[2430.544147] Scaffolding node -1850000
[2430.544555] Scaffolding node -1840000
[2430.544961] Scaffolding node -1830000
[2430.554104] Scaffolding node -1820000
[2430.554503] Scaffolding node -1810000
[2430.554899] Scaffolding node -1800000
[2430.555290] Scaffolding node -1790000
[2430.555697] Scaffolding node -1780000
[2430.556088] Scaffolding node -1770000
[2430.556476] Scaffolding node -1760000
[2430.556864] Scaffolding node -1750000
[2430.557260] Scaffolding node -1740000
[2430.557654] Scaffolding node -1730000
[2430.558049] Scaffolding node -1720000
[2430.558439] Scaffolding node -1710000
[2430.558834] Scaffolding node -1700000
[2430.574008] Scaffolding node -1690000
[2430.574400] Scaffolding node -1680000
[2430.574803] Scaffolding node -1670000
[2430.575207] Scaffolding node -1660000
[2430.575604] Scaffolding node -1650000
[2430.575997] Scaffolding node -1640000
[2430.601466] Scaffolding node -1630000
[2430.601864] Scaffolding node -1620000
[2430.602260] Scaffolding node -1610000
[2430.602649] Scaffolding node -1600000
[2430.603048] Scaffolding node -1590000
[2430.603449] Scaffolding node -1580000
[2430.603843] Scaffolding node -1570000
[2430.604244] Scaffolding node -1560000
[2430.604640] Scaffolding node -1550000
[2430.605031] Scaffolding node -1540000
[2430.605436] Scaffolding node -1530000
[2430.605849] Scaffolding node -1520000
[2430.606245] Scaffolding node -1510000
[2430.606637] Scaffolding node -1500000
[2430.607024] Scaffolding node -1490000
[2430.607436] Scaffolding node -1480000
[2430.607827] Scaffolding node -1470000
[2430.621338] Scaffolding node -1460000
[2430.621720] Scaffolding node -1450000
[2430.622106] Scaffolding node -1440000
[2430.622487] Scaffolding node -1430000
[2430.622870] Scaffolding node -1420000
[2430.623258] Scaffolding node -1410000
[2430.623632] Scaffolding node -1400000
[2430.624001] Scaffolding node -1390000
[2430.624393] Scaffolding node -1380000
[2430.624771] Scaffolding node -1370000
[2430.625161] Scaffolding node -1360000
[2430.625530] Scaffolding node -1350000
[2430.625910] Scaffolding node -1340000
[2430.626278] Scaffolding node -1330000
[2430.626649] Scaffolding node -1320000
[2430.627027] Scaffolding node -1310000
[2430.627403] Scaffolding node -1300000
[2430.627785] Scaffolding node -1290000
[2430.628168] Scaffolding node -1280000
[2430.628543] Scaffolding node -1270000
[2430.628918] Scaffolding node -1260000
[2430.629307] Scaffolding node -1250000
[2430.629698] Scaffolding node -1240000
[2430.630079] Scaffolding node -1230000
[2430.630460] Scaffolding node -1220000
[2430.630841] Scaffolding node -1210000
[2430.631230] Scaffolding node -1200000
[2430.631614] Scaffolding node -1190000
[2430.649616] Scaffolding node -1180000
[2430.650028] Scaffolding node -1170000
[2430.650416] Scaffolding node -1160000
[2430.650794] Scaffolding node -1150000
[2430.651177] Scaffolding node -1140000
[2430.651563] Scaffolding node -1130000
[2430.651952] Scaffolding node -1120000
[2430.652339] Scaffolding node -1110000
[2430.652723] Scaffolding node -1100000
[2430.653108] Scaffolding node -1090000
[2430.653503] Scaffolding node -1080000
[2430.653893] Scaffolding node -1070000
[2430.654276] Scaffolding node -1060000
[2430.654665] Scaffolding node -1050000
[2430.655068] Scaffolding node -1040000
[2430.655450] Scaffolding node -1030000
[2430.655834] Scaffolding node -1020000
[2430.656205] Scaffolding node -1010000
[2430.656595] Scaffolding node -1000000
[2430.656971] Scaffolding node -990000
[2430.657361] Scaffolding node -980000
[2430.657735] Scaffolding node -970000
[2430.658112] Scaffolding node -960000
[2430.658481] Scaffolding node -950000
[2430.658856] Scaffolding node -940000
[2430.659242] Scaffolding node -930000
[2430.659620] Scaffolding node -920000
[2430.659995] Scaffolding node -910000
[2430.666640] Scaffolding node -900000
[2430.667021] Scaffolding node -890000
[2430.667406] Scaffolding node -880000
[2430.667787] Scaffolding node -870000
[2430.668157] Scaffolding node -860000
[2430.668533] Scaffolding node -850000
[2430.669378] Scaffolding node -840000
[2430.669750] Scaffolding node -830000
[2430.670123] Scaffolding node -820000
[2430.670496] Scaffolding node -810000
[2430.670865] Scaffolding node -800000
[2430.671236] Scaffolding node -790000
[2430.671614] Scaffolding node -780000
[2430.678318] Scaffolding node -770000
[2430.678685] Scaffolding node -760000
[2430.679078] Scaffolding node -750000
[2430.679455] Scaffolding node -740000
[2430.679824] Scaffolding node -730000
[2430.680199] Scaffolding node -720000
[2430.680567] Scaffolding node -710000
[2430.680936] Scaffolding node -700000
[2430.681311] Scaffolding node -690000
[2430.681681] Scaffolding node -680000
[2430.682056] Scaffolding node -670000
[2430.682418] Scaffolding node -660000
[2430.682798] Scaffolding node -650000
[2430.683166] Scaffolding node -640000
[2430.683542] Scaffolding node -630000
[2430.683908] Scaffolding node -620000
[2430.684294] Scaffolding node -610000
[2430.684668] Scaffolding node -600000
[2430.685037] Scaffolding node -590000
[2430.685417] Scaffolding node -580000
[2430.685789] Scaffolding node -570000
[2430.686164] Scaffolding node -560000
[2430.693089] Scaffolding node -550000
[2430.693463] Scaffolding node -540000
[2430.693833] Scaffolding node -530000
[2430.694206] Scaffolding node -520000
[2430.694574] Scaffolding node -510000
[2430.694946] Scaffolding node -500000
[2430.695316] Scaffolding node -490000
[2430.695688] Scaffolding node -480000
[2430.696059] Scaffolding node -470000
[2430.696423] Scaffolding node -460000
[2430.696791] Scaffolding node -450000
[2430.697174] Scaffolding node -440000
[2430.703670] Scaffolding node -430000
[2430.704046] Scaffolding node -420000
[2430.704433] Scaffolding node -410000
[2430.704809] Scaffolding node -400000
[2430.705181] Scaffolding node -390000
[2430.705547] Scaffolding node -380000
[2430.705919] Scaffolding node -370000
[2430.706287] Scaffolding node -360000
[2430.706651] Scaffolding node -350000
[2430.707020] Scaffolding node -340000
[2430.707399] Scaffolding node -330000
[2430.707776] Scaffolding node -320000
[2430.708155] Scaffolding node -310000
[2430.708526] Scaffolding node -300000
[2430.708895] Scaffolding node -290000
[2430.709275] Scaffolding node -280000
[2430.709642] Scaffolding node -270000
[2430.710000] Scaffolding node -260000
[2430.710364] Scaffolding node -250000
[2430.710730] Scaffolding node -240000
[2430.711096] Scaffolding node -230000
[2430.711468] Scaffolding node -220000
[2430.711839] Scaffolding node -210000
[2430.712214] Scaffolding node -200000
[2430.721846] Scaffolding node -190000
[2430.722212] Scaffolding node -180000
[2430.722583] Scaffolding node -170000
[2430.722949] Scaffolding node -160000
[2430.723315] Scaffolding node -150000
[2430.723681] Scaffolding node -140000
[2430.724045] Scaffolding node -130000
[2430.724411] Scaffolding node -120000
[2430.724774] Scaffolding node -110000
[2430.725136] Scaffolding node -100000
[2430.725504] Scaffolding node -90000
[2430.725866] Scaffolding node -80000
[2430.726226] Scaffolding node -70000
[2430.726588] Scaffolding node -60000
[2430.726951] Scaffolding node -50000
[2430.727316] Scaffolding node -40000
[2430.727672] Scaffolding node -30000
[2430.738690] Scaffolding node -20000
[2430.739057] Scaffolding node -10000
[2430.739419] Scaffolding node 0
[2430.742295] Scaffolding node 10000
[2430.744928] Scaffolding node 20000
[2430.747558] Scaffolding node 30000
[2430.750083] Scaffolding node 40000
[2430.752454] Scaffolding node 50000
[2430.764636] Scaffolding node 60000
[2430.767260] Scaffolding node 70000
[2430.769911] Scaffolding node 80000
[2430.772766] Scaffolding node 90000
[2430.775497] Scaffolding node 100000
[2430.778074] Scaffolding node 110000
[2430.780794] Scaffolding node 120000
[2430.783435] Scaffolding node 130000
[2430.786320] Scaffolding node 140000
[2430.789259] Scaffolding node 150000
[2430.792232] Scaffolding node 160000
[2430.794685] Scaffolding node 170000
[2430.797621] Scaffolding node 180000
[2430.800244] Scaffolding node 190000
[2430.802823] Scaffolding node 200000
[2430.805553] Scaffolding node 210000
[2430.808973] Scaffolding node 220000
[2430.823786] Scaffolding node 230000
[2430.826583] Scaffolding node 240000
[2430.829509] Scaffolding node 250000
[2430.832211] Scaffolding node 260000
[2430.835276] Scaffolding node 270000
[2430.838079] Scaffolding node 280000
[2430.841002] Scaffolding node 290000
[2430.843579] Scaffolding node 300000
[2430.846685] Scaffolding node 310000
[2430.849919] Scaffolding node 320000
[2430.852925] Scaffolding node 330000
[2430.856018] Scaffolding node 340000
[2430.858972] Scaffolding node 350000
[2430.862357] Scaffolding node 360000
[2430.865786] Scaffolding node 370000
[2430.869279] Scaffolding node 380000
[2430.872366] Scaffolding node 390000
[2430.875408] Scaffolding node 400000
[2430.898345] Scaffolding node 410000
[2430.901352] Scaffolding node 420000
[2430.903945] Scaffolding node 430000
[2430.906953] Scaffolding node 440000
[2430.910298] Scaffolding node 450000
[2430.927833] Scaffolding node 460000
[2430.931351] Scaffolding node 470000
[2430.934143] Scaffolding node 480000
[2430.939363] Scaffolding node 490000
[2430.942121] Scaffolding node 500000
[2430.946805] Scaffolding node 510000
[2430.951255] Scaffolding node 520000
[2430.963572] Scaffolding node 530000
[2430.966451] Scaffolding node 540000
[2430.969991] Scaffolding node 550000
[2430.972996] Scaffolding node 560000
[2430.975964] Scaffolding node 570000
[2430.995321] Scaffolding node 580000
[2430.998611] Scaffolding node 590000
[2431.002202] Scaffolding node 600000
[2431.005531] Scaffolding node 610000
[2431.008391] Scaffolding node 620000
[2431.027486] Scaffolding node 630000
[2431.031075] Scaffolding node 640000
[2431.034414] Scaffolding node 650000
[2431.053871] Scaffolding node 660000
[2431.057089] Scaffolding node 670000
[2431.060302] Scaffolding node 680000
[2431.064108] Scaffolding node 690000
[2431.067713] Scaffolding node 700000
[2431.070985] Scaffolding node 710000
[2431.074405] Scaffolding node 720000
[2431.077536] Scaffolding node 730000
[2431.081020] Scaffolding node 740000
[2431.084554] Scaffolding node 750000
[2431.088133] Scaffolding node 760000
[2431.091801] Scaffolding node 770000
[2431.095501] Scaffolding node 780000
[2431.099079] Scaffolding node 790000
[2431.102338] Scaffolding node 800000
[2431.105613] Scaffolding node 810000
[2431.108946] Scaffolding node 820000
[2431.112295] Scaffolding node 830000
[2431.115446] Scaffolding node 840000
[2431.118965] Scaffolding node 850000
[2431.122848] Scaffolding node 860000
[2431.126739] Scaffolding node 870000
[2431.130060] Scaffolding node 880000
[2431.133813] Scaffolding node 890000
[2431.137328] Scaffolding node 900000
[2431.140992] Scaffolding node 910000
[2431.144891] Scaffolding node 920000
[2431.148767] Scaffolding node 930000
[2431.152630] Scaffolding node 940000
[2431.156123] Scaffolding node 950000
[2431.159944] Scaffolding node 960000
[2431.163924] Scaffolding node 970000
[2431.167571] Scaffolding node 980000
[2431.171488] Scaffolding node 990000
[2431.175005] Scaffolding node 1000000
[2431.178765] Scaffolding node 1010000
[2431.182636] Scaffolding node 1020000
[2431.186302] Scaffolding node 1030000
[2431.189928] Scaffolding node 1040000
[2431.193883] Scaffolding node 1050000
[2431.197868] Scaffolding node 1060000
[2431.201541] Scaffolding node 1070000
[2431.205441] Scaffolding node 1080000
[2431.209274] Scaffolding node 1090000
[2431.213315] Scaffolding node 1100000
[2431.217653] Scaffolding node 1110000
[2431.221544] Scaffolding node 1120000
[2431.225493] Scaffolding node 1130000
[2431.229905] Scaffolding node 1140000
[2431.234192] Scaffolding node 1150000
[2431.238220] Scaffolding node 1160000
[2431.242548] Scaffolding node 1170000
[2431.247409] Scaffolding node 1180000
[2431.251745] Scaffolding node 1190000
[2431.255259] Scaffolding node 1200000
[2431.259681] Scaffolding node 1210000
[2431.263863] Scaffolding node 1220000
[2431.267494] Scaffolding node 1230000
[2431.271654] Scaffolding node 1240000
[2431.275574] Scaffolding node 1250000
[2431.279856] Scaffolding node 1260000
[2431.284212] Scaffolding node 1270000
[2431.287[13.218321] === Threaded in 3.875731 s
[13.231891] Correcting graph with cutoff 0.200000
[13.235736] Determining eligible starting points
[13.287647] Done listing starting nodes
[13.287730] Initializing todo lists
[13.295837] Done with initilization
[13.295918] Activating arc lookup table
[13.306154] Done activating arc lookup table
[13.359803] 10000 / 88214 nodes visited
[13.390286] 20000 / 88214 nodes visited
[13.419911] 30000 / 88214 nodes visited
[13.431959] 40000 / 88214 nodes visited
[13.442740] 50000 / 88214 nodes visited
[13.451176] 60000 / 88214 nodes visited
[13.453918] 70000 / 88214 nodes visited
[13.456222] 80000 / 88214 nodes visited
[13.458343] Concatenation...
[13.461428] Renumbering nodes
[13.461490] Initial node count 88214
[13.462972] Removed 2495 null nodes
[13.463015] Concatenation over!
[13.463045] Clipping short tips off graph, drastic
[13.509660] Concatenation...
[13.535326] Renumbering nodes
[13.535408] Initial node count 85719
[13.541856] Removed 42493 null nodes
[13.541940] Concatenation over!
[13.541971] 43226 nodes left
[13.542040] Writing into graph file .//Graph2...
757] Scaffolding node 1280000
[2431.295914] Scaffolding node 1290000
[2431.300576] Scaffolding node 1300000
[2431.304829] Scaffolding node 1310000
[2431.309137] Scaffolding node 1320000
[2431.313342] Scaffolding node 1330000
[2431.317577] Scaffolding node 1340000
[2431.322107] Scaffolding node 1350000
[2431.326383] Scaffolding node 1360000
[2431.330678] Scaffolding node 1370000
[2431.335061] Scaffolding node 1380000
[2431.339645] Scaffolding node 1390000
[2431.344288] Scaffolding node 1400000
[2431.348598] Scaffolding node 1410000
[2431.353506] Scaffolding node 1420000
[2431.357881] Scaffolding node 1430000
[2431.362656] Scaffolding node 1440000
[2431.367743] Scaffolding node 1450000
[2431.372922] Scaffolding node 1460000
[2431.377322] Scaffolding node 1470000
[2431.382005] Scaffolding node 1480000
[2431.386921] Scaffolding node 1490000
[2431.391338] Scaffolding node 1500000
[2431.396149] Scaffolding node 1510000
[2431.401239] Scaffolding node 1520000
[2431.406378] Scaffolding node 1530000
[2431.411545] Scaffolding node 1540000
[2431.416431] Scaffolding node 1550000
[2431.421589] Scaffolding node 1560000
[2431.426820] Scaffolding node 1570000
[2431.431566] Scaffolding node 1580000
[2431.437130] Scaffolding node 1590000
[2431.442790] Scaffolding node 1600000
[2431.447649] Scaffolding node 1610000
[2431.453059] Scaffolding node 1620000
[2431.458105] Scaffolding node 1630000
[2431.463280] Scaffolding node 1640000
[2431.468171] Scaffolding node 1650000
[2431.473652] Scaffolding node 1660000
[2431.479033] Scaffolding node 1670000
[2431.484396] Scaffolding node 1680000
[2431.489425] Scaffolding node 1690000
[2431.494864] Scaffolding node 1700000
[2431.500439] Scaffolding node 1710000
[2431.505773] Scaffolding node 1720000
[2431.511380] Scaffolding node 1730000
[2431.517325] Scaffolding node 1740000
[2431.523061] Scaffolding node 1750000
[2431.529084] Scaffolding node 1760000
[2431.534442] Scaffolding node 1770000
[2431.540389] Scaffolding node 1780000
[2431.545788] Scaffolding node 1790000
[2431.551434] Scaffolding node 1800000
[2431.557204] Scaffolding node 1810000
[2431.562820] Scaffolding node 1820000
[2431.568443] Scaffolding node 1830000
[2431.574676] Scaffolding node 1840000
[2431.580723] Scaffolding node 1850000
[2431.586782] Scaffolding node 1860000
[2431.604279] Scaffolding node 1870000
[2431.611084] Scaffolding node 1880000
[2431.633392] Scaffolding node 1890000
[2431.639334] Scaffolding node 1900000
[2431.645377] Scaffolding node 1910000
[2431.668117] Scaffolding node 1920000
[2431.674169] Scaffolding node 1930000
[2431.697205] Scaffolding node 1940000
[2431.703700] Scaffolding node 1950000
[2431.709565] Scaffolding node 1960000
[2431.732325] Scaffolding node 1970000
[2431.738613] Scaffolding node 1980000
[2431.761239] Scaffolding node 1990000
[2431.767805] Scaffolding node 2000000
[2431.773879] Scaffolding node 2010000
[2431.796263] Scaffolding node 2020000
[2431.802685] Scaffolding node 2030000
[2431.823798] Scaffolding node 2040000
[2431.830071] Scaffolding node 2050000
[2431.852752] Scaffolding node 2060000
[2431.859626] Scaffolding node 2070000
[2431.866728] Scaffolding node 2080000
[2431.873595] Scaffolding node 2090000
[2431.881066] Scaffolding node 2100000
[2431.888613] Scaffolding node 2110000
[2431.895788] Scaffolding node 2120000
[2431.903410] Scaffolding node 2130000
[2431.910144] Scaffolding node 2140000
[2431.918276] Scaffolding node 2150000
[2431.925557] Scaffolding node 2160000
[2431.932982] Scaffolding node 2170000
[2431.940283] Scaffolding node 2180000
[2431.947437] Scaffolding node 2190000
[2431.955051] Scaffolding node 2200000
[2431.962915] Scaffolding node 2210000
[2431.969800] Scaffolding node 2220000
[2431.977317] Scaffolding node 2230000
[2431.984123] Scaffolding node 2240000
[2431.991331] Scaffolding node 2250000
[2431.999074] Scaffolding node 2260000
[2432.007245] Scaffolding node 2270000
[2432.014792] Scaffolding node 2280000
[2432.022166] Scaffolding node 2290000
[2432.030051] Scaffolding node 2300000
[2432.038314] Scaffolding node 2310000
[2432.046456] Scaffolding node 2320000
[2432.0544[14.263819] Measuring median coverage depth...
[14.291946] Median coverage depth = 2.000000
[14.307543] Removing contigs with coverage < 1.000000...
[14.308770] Concatenation...
[14.310113] Renumbering nodes
[14.310124] Initial node count 43226
[14.310195] Removed 0 null nodes
[14.310203] Concatenation over!
[14.311379] Concatenation...
[14.312532] Renumbering nodes
[14.312542] Initial node count 43226
[14.312611] Removed 0 null nodes
[14.312619] Concatenation over!
[14.312625] Clipping short tips off graph, drastic
[14.314951] Concatenation...
[14.328628] Renumbering nodes
[14.328682] Initial node count 43226
[14.328779] Removed 0 null nodes
[14.328812] Concatenation over!
[14.328843] 43226 nodes left
[14.328873] Read coherency...
[14.330096] Identifying unique nodes
[14.331297] Done, 41550 unique nodes counted
[14.331334] Trimming read tips
[14.333267] Renumbering nodes
[14.333306] Initial node count 43226
[14.333400] Removed 0 null nodes
[14.333432] Confronted to 0 multiple hits and 0 null over 0
[14.333462] Read coherency over!
[14.333994] Starting pebble resolution...
[14.335515] Computing read to node mapping array sizes
[14.340531] Computing read to node mappings
[14.362127] Estimating library insert lengths...
[14.362603] Done
[14.362631] Computing direct node to node mappings
[14.362779] Scaffolding node -40000
[14.363344] Scaffolding node -30000
[14.364124] Scaffolding node -20000
[14.365145] Scaffolding node -10000
[14.366371] Scaffolding node 0
[14.368111] Scaffolding node 10000
[14.369722] Scaffolding node 20000
[14.371083] Scaffolding node 30000
[14.384266] Scaffolding node 40000
[14.385008] === Nodes Scaffolded in 0.022374 s
[14.389059] Preparing to correct graph with cutoff 0.200000
[14.439553] Cleaning memory
[14.439670] Deactivating local correction settings
[14.440286] Pebble done.
[14.440325] Concatenation...
[14.441752] Renumbering nodes
[14.441791] Initial node count 43226
[14.442771] Removed 4 null nodes
[14.443335] Concatenation over!
[14.443373] Removing reference contigs with coverage < 1.000000...
[14.445300] Concatenation...
[14.453029] Renumbering nodes
[14.453083] Initial node count 43222
[14.453180] Removed 0 null nodes
[14.453750] Concatenation over!
[14.454283] Writing contigs into .//contigs.fa...
[15.168251] Writing into stats file .//stats.txt...
[15.353737] Writing into graph file .//LastGraph...
74] Scaffolding node 2330000
[2432.062685] Scaffolding node 2340000
[2432.070977] Scaffolding node 2350000
[2432.079129] Scaffolding node 2360000
[2432.088178] Scaffolding node 2370000
[2432.097209] Scaffolding node 2380000
[2432.105391] Scaffolding node 2390000
[2432.113972] Scaffolding node 2400000
[2432.122523] Scaffolding node 2410000
[2432.131139] Scaffolding node 2420000
[2432.139570] Scaffolding node 2430000
[2432.148500] Scaffolding node 2440000
[2432.157770] Scaffolding node 2450000
[2432.166482] Scaffolding node 2460000
[2432.175102] Scaffolding node 2470000
[2432.184858] Scaffolding node 2480000
[2432.194576] Scaffolding node 2490000
[2432.204556] Scaffolding node 2500000
[2432.213789] Scaffolding node 2510000
[2432.222807] Scaffolding node 2520000
[2432.232179] Scaffolding node 2530000
[2432.241763] Scaffolding node 2540000
[2432.252240] Scaffolding node 2550000
[2432.262107] Scaffolding node 2560000
[2432.272622] Scaffolding node 2570000
[2432.282915] Scaffolding node 2580000
[2432.293659] Scaffolding node 2590000
[2432.304191] Scaffolding node 2600000
[2432.314488] Scaffolding node 2610000
[2432.324564] Scaffolding node 2620000
[2432.334553] Scaffolding node 2630000
[2432.345675] Scaffolding node 2640000
[2432.356195] Scaffolding node 2650000
[2432.374294] Scaffolding node 2660000
[2432.384216] Scaffolding node 2670000
[2432.410590] Scaffolding node 2680000
[2432.437050] Scaffolding node 2690000
[2432.447646] Scaffolding node 2700000
[2432.470649] Scaffolding node 2710000
[2432.501725] Scaffolding node 2720000
[2432.512781] Scaffolding node 2730000
[2432.540379] Scaffolding node 2740000
[2432.563562] Scaffolding node 2750000
[2432.575982] Scaffolding node 2760000
[2432.587536] Scaffolding node 2770000
[2432.599103] Scaffolding node 2780000
[2432.610776] Scaffolding node 2790000
[2432.638976] Scaffolding node 2800000
[2432.651238] Scaffolding node 2810000
[2432.679154] Scaffolding node 2820000
[2432.695976] Scaffolding node 2830000
[2432.724459] Scaffolding node 2840000
[2432.753353] Scaffolding node 2850000
[2432.786490] Scaffolding node 2860000
[2432.799485] Scaffolding node 2870000
[2432.826107] Scaffolding node 2880000
[2432.863629] Scaffolding node 2890000
[2432.888621] Scaffolding node 2900000
[2432.917468] Scaffolding node 2910000
[2432.946468] Scaffolding node 2920000
[2432.960345] Scaffolding node 2930000
[2432.990003] Scaffolding node 2940000
[2433.019076] Scaffolding node 2950000
[2433.046428] Scaffolding node 2960000
[2433.076508] Scaffolding node 2970000
[2433.113812] Scaffolding node 2980000
[2433.139918] Scaffolding node 2990000
[2433.169883] Scaffolding node 3000000
[2433.184473] Scaffolding node 3010000
[2433.214845] Scaffolding node 3020000
[2433.244326] Scaffolding node 3030000
[2433.273021] Scaffolding node 3040000
[2433.287927] Scaffolding node 3050000
[2433.302778] Scaffolding node 3060000
[2433.317660] Scaffolding node 3070000
[2433.332592] Scaffolding node 3080000
[2433.347300] Scaffolding node 3090000
[2433.362816] Scaffolding node 3100000
[2433.377615] Scaffolding node 3110000
[2433.392694] Scaffolding node 3120000
[2433.408292] Scaffolding node 3130000
[2433.423429] Scaffolding node 3140000
[2433.438761] Scaffolding node 3150000
[2433.455078] Scaffolding node 3160000
[2433.471405] Scaffolding node 3170000
[2433.486572] Scaffolding node 3180000
[2433.501082] Scaffolding node 3190000
[2433.517253] Scaffolding node 3200000
[2433.532332] Scaffolding node 3210000
[2433.548131] Scaffolding node 3220000
[2433.563970] Scaffolding node 3230000
[2433.580259] Scaffolding node 3240000
[2433.597032] Scaffolding node 3250000
[2433.612858] Scaffolding node 3260000
[2433.628959] Scaffolding node 3270000
[2433.645175] Scaffolding node 3280000
[2433.663447] Scaffolding node 3290000
[2433.680031] Scaffolding node 3300000
[2433.697239] Scaffolding node 3310000
[2433.713953] Scaffolding node 3320000
[2433.742130] Scaffolding node 3330000
[2433.772519] Scaffolding node 3340000
[2433.809184] Scaffolding node 3350000
[2433.848333] Scaffolding node 3360000
[2433.882356] Scaffolding node 3370000
[2433.93135[16.297073] Estimated Coverage = 2.000000
[16.297085] Estimated Coverage cutoff = 1.000000
Final graph has 43222 nodes and n50 of 120, max 469, total 5013597, using 98674/100000 reads
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_31.fa
START-velveth
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velveth ./ 31 -fastq /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq ;
[0.000000] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq;
[0.397413] 50000 sequences found
[0.397487] Done
[0.410450] Reading read set file .//Sequences;
[0.419968] 50000 sequences found
[0.516012] Done
[0.516024] 50000 sequences in total.
[0.516403] Writing into roadmap file .//Roadmaps...
[0.674156] Inputting sequences...
[0.674167] Inputting sequence 0 / 50000
[1.916500] === Sequences loaded in 1.242344 s
[1.916741] Done inputting sequences
[1.916781] Destroying splay table
[1.932754] Splay table destroyed
START-velvetg
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500
[0.000000] Reading roadmap file .//Roadmaps
[0.094847] 50000 roadmaps read
[0.095037] Creating insertion markers
[0.096557] Ordering insertion markers
[0.098311] Counting preNodes
[0.099564] 49291 preNodes counted, creating them now
6] Scaffolding node 3380000
[2433.966020] Scaffolding node 3390000
[2433.992776] Scaffolding node 3400000
[2434.011564] Scaffolding node 3410000
[2434.030873] Scaffolding node 3420000
[2434.050484] Scaffolding node 3430000
[2434.069525] Scaffolding node 3440000
[2434.087038] Scaffolding node 3450000
[2434.105816] Scaffolding node 3460000
[2434.124109] Scaffolding node 3470000
[2434.144038] Scaffolding node 3480000
[2434.163933] Scaffolding node 3490000
[2434.183362] Scaffolding node 3500000
[2434.203188] Scaffolding node 3510000
[2434.222608] Scaffolding node 3520000
[2434.242107] Scaffolding node 3530000
[2434.261678] Scaffolding node 3540000
[2434.282702] Scaffolding node 3550000
[2434.303468] Scaffolding node 3560000
[2434.323292] Scaffolding node 3570000
[2434.344755] Scaffolding node 3580000
[2434.365608] Scaffolding node 3590000
[2434.430354] Scaffolding node 3600000
[2434.508680] Scaffolding node 3610000
[2434.532226] Scaffolding node 3620000
[2434.553944] Scaffolding node 3630000
[2434.590536] Scaffolding node 3640000
[2434.641400] Scaffolding node 3650000
[2434.664799] Scaffolding node 3660000
[2434.697486] Scaffolding node 3670000
[2434.717847] Scaffolding node 3680000
[2434.775894] Scaffolding node 3690000
[2434.804751] Scaffolding node 3700000
[2434.824882] Scaffolding node 3710000
[2434.847421] Scaffolding node 3720000
[2434.881560] Scaffolding node 3730000
[2434.903265] Scaffolding node 3740000
[2434.925751] Scaffolding node 3750000
[2434.963155] Scaffolding node 3760000
[2434.984782] Scaffolding node 3770000
[2435.006746] Scaffolding node 3780000
[2435.029158] Scaffolding node 3790000
[2435.050500] Scaffolding node 3800000
[2435.092110] Scaffolding node 3810000
[2435.141494] Scaffolding node 3820000
[2435.191567] Scaffolding node 3830000
[2435.230763] Scaffolding node 3840000
[2435.270152] Scaffolding node 3850000
[2435.293531] Scaffolding node 3860000
[2435.314468] Scaffolding node 3870000
[2435.335586] Scaffolding node 3880000
[2435.356543] Scaffolding node 3890000
[2435.382957] Scaffolding node 3900000
[2435.423511] Scaffolding node 3910000
[2435.464456] Scaffolding node 3920000
[2435.486160] Scaffolding node 3930000
[2435.506898] Scaffolding node 3940000
[2435.529794] Scaffolding node 3950000
[2435.551629] Scaffolding node 3960000
[2435.572875] Scaffolding node 3970000
[2435.594188] Scaffolding node 3980000
[2435.615612] Scaffolding node 3990000
[2435.637390] Scaffolding node 4000000
[2435.660282] Scaffolding node 4010000
[2435.681666] Scaffolding node 4020000
[2435.702616] Scaffolding node 4030000
[2435.724743] Scaffolding node 4040000
[2435.747212] Scaffolding node 4050000
[2435.769031] Scaffolding node 4060000
[2435.791932] Scaffolding node 4070000
[2435.813527] Scaffolding node 4080000
[2435.835684] Scaffolding node 4090000
[2435.857539] Scaffolding node 4100000
[2435.879993] Scaffolding node 4110000
[2435.903108] Scaffolding node 4120000
[2435.926123] Scaffolding node 4130000
[2435.948190] Scaffolding node 4140000
[2435.970090] Scaffolding node 4150000
[2435.990851] Scaffolding node 4160000
[2436.013203] Scaffolding node 4170000
[2436.044217] Scaffolding node 4180000
[2436.065619] Scaffolding node 4190000
[2436.099238] Scaffolding node 4200000
[2436.122349] Scaffolding node 4210000
[2436.143276] Scaffolding node 4220000
[2436.175046] Scaffolding node 4230000
[2436.232346] Scaffolding node 4240000
[2436.270843] Scaffolding node 4250000
[2436.308633] Scaffolding node 4260000
[2436.369909] Scaffolding node 4270000
[2436.407559] Scaffolding node 4280000
[2436.449002] Scaffolding node 4290000
[2436.494554] Scaffolding node 4300000
[2436.531475] Scaffolding node 4310000
[2436.554054] Scaffolding node 4320000
[2436.591013] Scaffolding node 4330000
[2436.627803] Scaffolding node 4340000
[2436.664810] Scaffolding node 4350000
[2436.687164] Scaffolding node 4360000
[2436.710192] Scaffolding node 4370000
[2436.732516] Scaffolding node 4380000
[2436.753704] Scaffolding node 4390000
[2436.775117] Scaffolding node 4400000
[2436.796125] Scaffolding node 4410000
[2436.817325] Scaffolding node 4420000
[2436.854921[0.206016] Adjusting marker info...
[0.206504] Connecting preNodes
[0.210130] Cleaning up memory
[0.210159] Done creating preGraph
[0.210163] Concatenation...
[0.222028] Renumbering preNodes
[0.222034] Initial preNode count 49291
[0.223338] Destroyed 15649 preNodes
[0.223344] Concatenation over!
[0.223347] Clipping short tips off preGraph
[0.250100] Concatenation...
[0.256161] Renumbering preNodes
[0.256167] Initial preNode count 33642
[0.256985] Destroyed 14634 preNodes
[0.256989] Concatenation over!
[0.256992] 8636 tips cut off
[0.256996] 19008 nodes left
[0.257032] Writing into pregraph file .//PreGraph...
[0.440081] Reading read set file .//Sequences;
[0.450159] 50000 sequences found
[0.501370] Done
[0.706375] Reading pre-graph file .//PreGraph
[0.706409] Graph has 19008 nodes and 50000 sequences
[0.791664] Scanning pre-graph file .//PreGraph for k-mers
[0.816117] 1339993 kmers found
[0.952485] Sorting kmer occurence table ...
[1.626861] Sorting done.
[1.626962] Computing acceleration table...
[1.679587] Computing offsets...
[1.686759] Ghost Threading through reads 0 / 50000
[2.829097] === Ghost-Threaded in 1.142337 s
[2.829201] Threading through reads 0 / 50000
] Scaffolding node 4430000
[2436.892473] Scaffolding node 4440000
[2436.925606] Scaffolding node 4450000
[2436.979018] Scaffolding node 4460000
[2437.016760] Scaffolding node 4470000
[2437.038592] Scaffolding node 4480000
[2437.059359] Scaffolding node 4490000
[2437.080326] Scaffolding node 4500000
[2437.102415] Scaffolding node 4510000
[2437.155184] Scaffolding node 4520000
[2437.192438] Scaffolding node 4530000
[2437.225077] Scaffolding node 4540000
[2437.278362] Scaffolding node 4550000
[2437.316632] Scaffolding node 4560000
[2437.353693] Scaffolding node 4570000
[2437.407098] Scaffolding node 4580000
[2437.432753] Scaffolding node 4590000
[2437.453673] Scaffolding node 4600000
[2437.490272] Scaffolding node 4610000
[2437.527833] Scaffolding node 4620000
[2437.550076] Scaffolding node 4630000
[2437.603889] Scaffolding node 4640000
[2437.640923] Scaffolding node 4650000
[2437.694731] Scaffolding node 4660000
[2437.747750] Scaffolding node 4670000
[2437.784960] Scaffolding node 4680000
[2437.807120] Scaffolding node 4690000
[2437.828645] Scaffolding node 4700000
[2437.850328] Scaffolding node 4710000
[2437.871447] Scaffolding node 4720000
[2437.892960] Scaffolding node 4730000
[2437.913534] Scaffolding node 4740000
[2437.935320] Scaffolding node 4750000
[2437.981118] Scaffolding node 4760000
[2438.027682] Scaffolding node 4770000
[2438.064435] Scaffolding node 4780000
[2438.109679] Scaffolding node 4790000
[2438.146363] Scaffolding node 4800000
[2438.183706] Scaffolding node 4810000
[2438.237109] Scaffolding node 4820000
[2438.274279] Scaffolding node 4830000
[2438.327092] Scaffolding node 4840000
[2438.364405] Scaffolding node 4850000
[2438.401779] Scaffolding node 4860000
[2438.434491] Scaffolding node 4870000
[2438.455245] Scaffolding node 4880000
[2438.475668] Scaffolding node 4890000
[2438.500595] Scaffolding node 4900000
[2438.521568] Scaffolding node 4910000
[2438.542116] Scaffolding node 4920000
[2438.579449] Scaffolding node 4930000
[2438.616567] Scaffolding node 4940000
[2438.653595] Scaffolding node 4950000
[2438.674193] Scaffolding node 4960000
[2438.694972] Scaffolding node 4970000
[2438.716420] Scaffolding node 4980000
[2438.736446] Scaffolding node 4990000
[2438.757334] Scaffolding node 5000000
[2438.778519] Scaffolding node 5010000
[2438.799863] Scaffolding node 5020000
[2438.829002] Scaffolding node 5030000
[2438.849900] Scaffolding node 5040000
[2438.871383] Scaffolding node 5050000
[2438.900095] Scaffolding node 5060000
[2438.921036] Scaffolding node 5070000
[2438.957797] Scaffolding node 5080000
[2438.994474] Scaffolding node 5090000
[2439.030573] Scaffolding node 5100000
[2439.052108] Scaffolding node 5110000
[2439.072554] Scaffolding node 5120000
[2439.093532] Scaffolding node 5130000
[2439.114834] Scaffolding node 5140000
[2439.136087] Scaffolding node 5150000
[2439.156082] Scaffolding node 5160000
[2439.176817] Scaffolding node 5170000
[2439.204788] Scaffolding node 5180000
[2439.225560] Scaffolding node 5190000
[2439.246723] Scaffolding node 5200000
[2439.283448] Scaffolding node 5210000
[2439.320091] Scaffolding node 5220000
[2439.357171] Scaffolding node 5230000
[2439.378485] Scaffolding node 5240000
[2439.400037] Scaffolding node 5250000
[2439.420946] Scaffolding node 5260000
[2439.441560] Scaffolding node 5270000
[2439.478032] Scaffolding node 5280000
[2439.502708] Scaffolding node 5290000
[2439.539484] Scaffolding node 5300000
[2439.560698] Scaffolding node 5310000
[2439.581722] Scaffolding node 5320000
[2439.602024] Scaffolding node 5330000
[2439.621979] Scaffolding node 5340000
[2439.642714] Scaffolding node 5350000
[2439.695356] Scaffolding node 5360000
[2439.731482] Scaffolding node 5370000
[2439.767629] Scaffolding node 5380000
[2439.804483] Scaffolding node 5390000
[2439.824530] Scaffolding node 5400000
[2439.860751] Scaffolding node 5410000
[2439.897337] Scaffolding node 5420000
[2439.934709] Scaffolding node 5430000
[2439.956100] Scaffolding node 5440000
[2439.976317] Scaffolding node 5450000
[2439.996558] Scaffolding node 5460000
[2440.016661] Scaffolding node 5470000
[2440.044516][4.077722] === Threaded in 1.248521 s
[4.082509] Correcting graph with cutoff 0.200000
[4.083047] Determining eligible starting points
[4.092410] Done listing starting nodes
[4.092476] Initializing todo lists
[4.093631] Done with initilization
[4.093683] Activating arc lookup table
[4.094316] Done activating arc lookup table
[4.163930] 10000 / 19008 nodes visited
[4.189028] Concatenation...
[4.202652] Renumbering nodes
[4.202709] Initial node count 19008
[4.202978] Removed 1975 null nodes
[4.203020] Concatenation over!
[4.203050] Clipping short tips off graph, drastic
[4.209557] Concatenation...
[4.211761] Renumbering nodes
[4.211810] Initial node count 17033
[4.212501] Removed 5982 null nodes
[4.221916] Concatenation over!
[4.221950] 11051 nodes left
[4.222020] Writing into graph file .//Graph2...
[4.411463] Measuring median coverage depth...
[4.414438] Median coverage depth = 1.054054
[4.414506] Removing contigs with coverage < 0.527027...
[4.414776] Concatenation...
[4.415102] Renumbering nodes
[4.415146] Initial node count 11051
[4.415201] Removed 0 null nodes
[4.415233] Concatenation over!
[4.415513] Concatenation...
[4.415751] Renumbering nodes
[4.415798] Initial node count 11051
[4.415848] Removed 0 null nodes
[4.415886] Concatenation over!
[4.415917] Clipping short tips off graph, drastic
[4.416472] Concatenation...
[4.416696] Renumbering nodes
[4.416739] Initial node count 11051
[4.416793] Removed 0 null nodes
[4.416827] Concatenation over!
[4.416856] 11051 nodes left
[4.416892] Read coherency...
[4.417000] Identifying unique nodes
[4.417295] Done, 9884 unique nodes counted
[4.417336] Trimming read tips
[4.417715] Renumbering nodes
[4.417756] Initial node count 11051
[4.417809] Removed 0 null nodes
[4.417840] Confronted to 0 multiple hits and 0 null over 0
[4.417876] Read coherency over!
[4.418192] Starting pebble resolution...
[4.418552] Computing read to node mapping array sizes
[4.419572] Computing read to node mappings
[4.420453] Estimating library insert lengths...
[4.420739] Done
[4.420784] Computing direct node to node mappings
[4.420864] Scaffolding node -10000
[4.421515] Scaffolding node 0
[4.422450] Scaffolding node 10000
[4.422730] === Nodes Scaffolded in 0.001917 s
[4.423389] Preparing to correct graph with cutoff 0.200000
[4.426371] Cleaning memory
[4.426422] Deactivating local correction settings
[4.426533] Pebble done.
[4.426567] Concatenation...
[4.426854] Renumbering nodes
[4.426896] Initial node count 11051
[4.426949] Removed 0 null nodes
[4.427031] Concatenation over!
[4.427074] Removing reference contigs with coverage < 0.527027...
[4.427501] Concatenation...
[4.427723] Renumbering nodes
[4.427765] Initial node count 11051
[4.427817] Removed 0 null nodes
[4.427900] Concatenation over!
[4.428240] Writing contigs into .//contigs.fa...
[4.581390] Writing into stats file .//stats.txt...
[4.608894] Writing into graph file .//LastGraph...
[4.806218] Estimated Coverage = 1.054054
[4.806232] Estimated Coverage cutoff = 0.527027
Final graph has 11051 nodes and n50 of 116, max 469, total 1197385, using 20217/50000 reads
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa
START-velveth
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velveth ./ 51 -fastq /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_1.out /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq ;
[0.000000] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_1.out;
[0.336173] 50000 sequences found
[0.336267] Done
[0.336317] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq;
[0.668328] 50000 sequences found
[0.668336] Done
[0.693436] Reading read set file .//Sequences;
[0.728045] 100000 sequences found
[0.919458] Done
[0.919468] 100000 sequences in total.
[0.919627] Writing into roadmap file .//Roadmaps...
Scaffolding node 5480000
[2440.089419] Scaffolding node 5490000
[2440.142004] Scaffolding node 5500000
[2440.177771] Scaffolding node 5510000
[2440.197817] Scaffolding node 5520000
[2440.218749] Scaffolding node 5530000
[2440.271166] Scaffolding node 5540000
[2440.307590] Scaffolding node 5550000
[2440.328523] Scaffolding node 5560000
[2440.349257] Scaffolding node 5570000
[2440.370212] Scaffolding node 5580000
[2440.390358] Scaffolding node 5590000
[2440.410545] Scaffolding node 5600000
[2440.451190] Scaffolding node 5610000
[2440.487475] Scaffolding node 5620000
[2440.507636] Scaffolding node 5630000
[2440.528460] Scaffolding node 5640000
[2440.548687] Scaffolding node 5650000
[2440.568082] Scaffolding node 5660000
[2440.593546] Scaffolding node 5670000
[2440.630567] Scaffolding node 5680000
[2440.666682] Scaffolding node 5690000
[2440.719636] Scaffolding node 5700000
[2440.755631] Scaffolding node 5710000
[2440.775780] Scaffolding node 5720000
[2440.796718] Scaffolding node 5730000
[2440.848430] Scaffolding node 5740000
[2440.883914] Scaffolding node 5750000
[2440.903313] Scaffolding node 5760000
[2440.923026] Scaffolding node 5770000
[2440.942855] Scaffolding node 5780000
[2440.963403] Scaffolding node 5790000
[2440.982746] Scaffolding node 5800000
[2441.018196] Scaffolding node 5810000
[2441.058726] Scaffolding node 5820000
[2441.078378] Scaffolding node 5830000
[2441.099446] Scaffolding node 5840000
[2441.119977] Scaffolding node 5850000
[2441.140396] Scaffolding node 5860000
[2441.160585] Scaffolding node 5870000
[2441.180463] Scaffolding node 5880000
[2441.224233] Scaffolding node 5890000
[2441.244078] Scaffolding node 5900000
[2441.264288] Scaffolding node 5910000
[2441.284106] Scaffolding node 5920000
[2441.303505] Scaffolding node 5930000
[2441.324052] Scaffolding node 5940000
[2441.343887] Scaffolding node 5950000
[2441.363171] Scaffolding node 5960000
[2441.382602] Scaffolding node 5970000
[2441.402074] Scaffolding node 5980000
[2441.437434] Scaffolding node 5990000
[2441.458361] Scaffolding node 6000000
[2441.493031] Scaffolding node 6010000
[2441.512506] Scaffolding node 6020000
[2441.539603] Scaffolding node 6030000
[2441.566589] Scaffolding node 6040000
[2441.586381] Scaffolding node 6050000
[2441.606905] Scaffolding node 6060000
[2441.627223] Scaffolding node 6070000
[2441.646622] Scaffolding node 6080000
[2441.682069] Scaffolding node 6090000
[2441.717821] Scaffolding node 6100000
[2441.753186] Scaffolding node 6110000
[2441.773626] Scaffolding node 6120000
[2441.793060] Scaffolding node 6130000
[2441.812628] Scaffolding node 6140000
[2441.832984] Scaffolding node 6150000
[2441.851866] Scaffolding node 6160000
[2441.871325] Scaffolding node 6170000
[2441.890105] Scaffolding node 6180000
[2441.908878] Scaffolding node 6190000
[2441.940519] Scaffolding node 6200000
[2441.960087] Scaffolding node 6210000
[2441.979532] Scaffolding node 6220000
[2441.998621] Scaffolding node 6230000
[2442.017937] Scaffolding node 6240000
[2442.037255] Scaffolding node 6250000
[2442.073011] Scaffolding node 6260000
[2442.123870] Scaffolding node 6270000
[2442.142978] Scaffolding node 6280000
[2442.162752] Scaffolding node 6290000
[2442.182291] Scaffolding node 6300000
[2442.201665] Scaffolding node 6310000
[2442.220547] Scaffolding node 6320000
[2442.251883] Scaffolding node 6330000
[2442.283900] Scaffolding node 6340000
[2442.318467] Scaffolding node 6350000
[2442.369604] Scaffolding node 6360000
[2442.404913] Scaffolding node 6370000
[2442.439578] Scaffolding node 6380000
[2442.457909] Scaffolding node 6390000
[2442.477403] Scaffolding node 6400000
[2442.504420] Scaffolding node 6410000
[2442.531221] Scaffolding node 6420000
[2442.566784] Scaffolding node 6430000
[2442.614543] Scaffolding node 6440000
[2442.634160] Scaffolding node 6450000
[2442.653082] Scaffolding node 6460000
[2442.671964] Scaffolding node 6470000
[2442.690772] Scaffolding node 6480000
[2442.709737] Scaffolding node 6490000
[2442.728184] Scaffolding node 6500000
[2442.747151] Scaffolding node 6510000
[2442.765966] Scaffolding node 6520000
[2442.784386] [1.147114] Inputting sequences...
[1.147470] Inputting sequence 0 / 100000
[4.270594] === Sequences loaded in 3.123482 s
[4.270895] Done inputting sequences
[4.270901] Destroying splay table
[4.302355] Splay table destroyed
START-velvetg
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500
[0.000001] Reading roadmap file .//Roadmaps
[0.133548] 100000 roadmaps read
[0.133783] Creating insertion markers
[0.136277] Ordering insertion markers
[0.138851] Counting preNodes
[0.140875] 54835 preNodes counted, creating them now
[0.603414] Adjusting marker info...
[0.604304] Connecting preNodes
[0.607187] Cleaning up memory
[0.607317] Done creating preGraph
[0.607354] Concatenation...
[0.609215] Renumbering preNodes
[0.609259] Initial preNode count 54835
[0.609844] Destroyed 583 preNodes
[0.609882] Concatenation over!
[0.609913] Clipping short tips off preGraph
[0.615939] Concatenation...
[0.616703] Renumbering preNodes
[0.616739] Initial preNode count 54252
[0.617110] Destroyed 46925 preNodes
[0.617153] Concatenation over!
[0.617182] 46784 tips cut off
[0.617209] 7327 nodes left
[0.617319] Writing into pregraph file .//PreGraph...
[0.655466] Reading read set file .//Sequences;
[0.674193] 100000 sequences found
[0.840457] Done
[1.104101] Reading pre-graph file .//PreGraph
[1.104221] Graph has 7327 nodes and 100000 sequences
[1.118893] Scanning pre-graph file .//PreGraph for k-mers
[1.147223] 312686 kmers found
[1.165274] Sorting kmer occurence table ...
[1.280545] Sorting done.
[1.280634] Computing acceleration table...
[1.309767] Computing offsets...
[1.311416] Ghost Threading through reads 0 / 100000
[3.059598] === Ghost-Threaded in 1.748182 s
[3.059704] Threading through reads 0 / 100000
Scaffolding node 6530000
[2442.818912] Scaffolding node 6540000
[2442.854076] Scaffolding node 6550000
[2442.889300] Scaffolding node 6560000
[2442.908232] Scaffolding node 6570000
[2442.927405] Scaffolding node 6580000
[2442.946714] Scaffolding node 6590000
[2442.965367] Scaffolding node 6600000
[2442.983950] Scaffolding node 6610000
[2443.002213] Scaffolding node 6620000
[2443.020544] Scaffolding node 6630000
[2443.055286] Scaffolding node 6640000
[2443.090118] Scaffolding node 6650000
[2443.125426] Scaffolding node 6660000
[2443.163911] Scaffolding node 6670000
[2443.199019] Scaffolding node 6680000
[2443.249664] Scaffolding node 6690000
[2443.283819] Scaffolding node 6700000
[2443.314539] Scaffolding node 6710000
[2443.348400] Scaffolding node 6720000
[2443.382707] Scaffolding node 6730000
[2443.412944] Scaffolding node 6740000
[2443.463484] Scaffolding node 6750000
[2443.482555] Scaffolding node 6760000
[2443.500847] Scaffolding node 6770000
[2443.519263] Scaffolding node 6780000
[2443.537687] Scaffolding node 6790000
[2443.555243] Scaffolding node 6800000
[2443.572962] Scaffolding node 6810000
[2443.607197] Scaffolding node 6820000
[2443.641448] Scaffolding node 6830000
[2443.675024] Scaffolding node 6840000
[2443.693363] Scaffolding node 6850000
[2443.711749] Scaffolding node 6860000
[2443.729701] Scaffolding node 6870000
[2443.748009] Scaffolding node 6880000
[2443.765646] Scaffolding node 6890000
[2443.791295] Scaffolding node 6900000
[2443.825483] Scaffolding node 6910000
[2443.855963] Scaffolding node 6920000
[2443.905775] Scaffolding node 6930000
[2443.939784] Scaffolding node 6940000
[2443.973183] Scaffolding node 6950000
[2444.007669] Scaffolding node 6960000
[2444.037957] Scaffolding node 6970000
[2444.080397] Scaffolding node 6980000
[2444.126924] Scaffolding node 6990000
[2444.160951] Scaffolding node 7000000
[2444.195076] Scaffolding node 7010000
[2444.233237] Scaffolding node 7020000
[2444.268012] Scaffolding node 7030000
[2444.315042] Scaffolding node 7040000
[2444.358015] Scaffolding node 7050000
[2444.375657] Scaffolding node 7060000
[2444.410258] Scaffolding node 7070000
[2444.429020] Scaffolding node 7080000
[2444.447326] Scaffolding node 7090000
[2444.466750] Scaffolding node 7100000
[2444.486311] Scaffolding node 7110000
[2444.504517] Scaffolding node 7120000
[2444.528911] Scaffolding node 7130000
[2444.546359] Scaffolding node 7140000
[2444.593676] Scaffolding node 7150000
[2444.620150] Scaffolding node 7160000
[2444.637970] Scaffolding node 7170000
[2444.673270] Scaffolding node 7180000
[2444.710155] Scaffolding node 7190000
[2444.771121] Scaffolding node 7200000
[2444.804181] Scaffolding node 7210000
[2444.821780] Scaffolding node 7220000
[2444.838815] Scaffolding node 7230000
[2444.856037] Scaffolding node 7240000
[2444.872976] Scaffolding node 7250000
[2444.889550] Scaffolding node 7260000
[2444.922903] Scaffolding node 7270000
[2444.966737] Scaffolding node 7280000
[2444.983739] Scaffolding node 7290000
[2445.001416] Scaffolding node 7300000
[2445.022203] Scaffolding node 7310000
[2445.045084] Scaffolding node 7320000
[2445.062405] Scaffolding node 7330000
[2445.120553] Scaffolding node 7340000
[2445.147361] Scaffolding node 7350000
[2445.165218] Scaffolding node 7360000
[2445.182096] Scaffolding node 7370000
[2445.201156] Scaffolding node 7380000
[2445.217462] Scaffolding node 7390000
[2445.234159] Scaffolding node 7400000
[2445.251739] Scaffolding node 7410000
[2445.268423] Scaffolding node 7420000
[2445.306308] Scaffolding node 7430000
[2445.329141] Scaffolding node 7440000
[2445.349925] Scaffolding node 7450000
[2445.368268] Scaffolding node 7460000
[2445.384515] Scaffolding node 7470000
[2445.417078] Scaffolding node 7480000
[2445.491301] Scaffolding node 7490000
[2445.537886] Scaffolding node 7500000
[2445.577623] Scaffolding node 7510000
[2445.609764] Scaffolding node 7520000
[2445.641980] Scaffolding node 7530000
[2445.658473] Scaffolding node 7540000
[2445.674164] Scaffolding node 7550000
[2446.835777] === Nodes Scaffolded in 16.751052 s
[2449.252000] Preparing to correct graph w[4.419332] === Threaded in 1.359628 s
[4.422727] Correcting graph with cutoff 0.200000
[4.422949] Determining eligible starting points
[4.426019] Done listing starting nodes
[4.426069] Initializing todo lists
[4.426372] Done with initilization
[4.426410] Activating arc lookup table
[4.426607] Done activating arc lookup table
[4.428592] Concatenation...
[4.428785] Renumbering nodes
[4.428819] Initial node count 7327
[4.428915] Removed 15 null nodes
[4.428951] Concatenation over!
[4.428984] Clipping short tips off graph, drastic
[4.430010] Concatenation...
[4.430431] Renumbering nodes
[4.430467] Initial node count 7312
[4.430804] Removed 7144 null nodes
[4.430840] Concatenation over!
[4.430871] 168 nodes left
[4.430938] Writing into graph file .//Graph2...
[4.434074] Measuring median coverage depth...
[4.447574] Median coverage depth = 2.129032
[4.447614] Removing contigs with coverage < 1.064516...
[4.447629] Concatenation...
[4.447641] Renumbering nodes
[4.447644] Initial node count 168
[4.447647] Removed 0 null nodes
[4.447650] Concatenation over!
[4.447655] Concatenation...
[4.447667] Renumbering nodes
[4.447673] Initial node count 168
[4.447680] Removed 0 null nodes
[4.447698] Concatenation over!
[4.447707] Clipping short tips off graph, drastic
[4.447726] Concatenation...
[4.447735] Renumbering nodes
[4.447754] Initial node count 168
[4.447762] Removed 0 null nodes
[4.447769] Concatenation over!
[4.447775] 168 nodes left
[4.447784] Read coherency...
[4.447790] Identifying unique nodes
[4.447812] Done, 165 unique nodes counted
[4.447820] Trimming read tips
[4.447831] Renumbering nodes
[4.447838] Initial node count 168
[4.447861] Removed 0 null nodes
[4.447870] Confronted to 0 multiple hits and 0 null over 0
[4.447876] Read coherency over!
[4.448408] Starting pebble resolution...
[4.448897] Computing read to node mapping array sizes
[4.449086] Computing read to node mappings
[4.449128] Estimating library insert lengths...
[4.449615] Done
[4.449625] Computing direct node to node mappings
[4.449651] Scaffolding node 0
[4.449697] === Nodes Scaffolded in 0.000065 s
[4.449736] Preparing to correct graph with cutoff 0.200000
[4.449809] Cleaning memory
[4.449823] Deactivating local correction settings
[4.449835] Pebble done.
[4.449842] Concatenation...
[4.449850] Renumbering nodes
[4.449859] Initial node count 168
[4.449866] Removed 0 null nodes
[4.449888] Concatenation over!
[4.449895] Removing reference contigs with coverage < 1.064516...
[4.449909] Concatenation...
[4.449918] Renumbering nodes
[4.449936] Initial node count 168
[4.449943] Removed 0 null nodes
[4.449950] Concatenation over!
[4.450479] Writing contigs into .//contigs.fa...
[4.453197] Writing into stats file .//stats.txt...
[4.463112] Writing into graph file .//LastGraph...
[4.466405] Estimated Coverage = 2.129032
[4.466419] Estimated Coverage cutoff = 1.064516
Final graph has 168 nodes and n50 of 163, max 319, total 25832, using 832/100000 reads
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_1.cv_51.fa
START-velveth
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velveth ./ 51 -fastq /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_8.out /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq ;
[0.000000] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/sample/sample.c_8.out;
[0.347733] 50000 sequences found
[0.347829] Done
[0.347887] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq;
[0.612849] 50000 sequences found
[0.612949] Done
[0.660759] Reading read set file .//Sequences;
[0.689060] 100000 sequences found
[0.795734] Done
[0.795827] 100000 sequences in total.
[0.796224] Writing into roadmap file .//Roadmaps...
[0.952236] Inputting sequences...
[0.952333] Inputting sequence 0 / 100000
[3.078091] === Sequences loaded in 2.125857 s
[3.078582] Done inputting sequences
[3.078657] Destroying splay table
[3.093977] Splay table destroyed
START-velvetg
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500
[0.000000] Reading roadmap file .//Roadmaps
[0.169712] 100000 roadmaps read
[0.169962] Creating insertion markers
[0.172272] Ordering insertion markers
[0.174450] Counting preNodes
[0.176086] 54835 preNodes counted, creating them now
[0.581456] Adjusting marker info...
[0.582401] Connecting preNodes
[0.585265] Cleaning up memory
[0.585374] Done creating preGraph
[0.585409] Concatenation...
[0.587267] Renumbering preNodes
[0.587306] Initial preNode count 54835
[0.587896] Destroyed 583 preNodes
[0.587936] Concatenation over!
[0.587965] Clipping short tips off preGraph
[0.594062] Concatenation...
[0.601113] Renumbering preNodes
[0.601118] Initial preNode count 54252
[0.601472] Destroyed 46925 preNodes
[0.601476] Concatenation over!
[0.601481] 46784 tips cut off
[0.601483] 7327 nodes left
[0.601517] Writing into pregraph file .//PreGraph...
[0.646842] Reading read set file .//Sequences;
[0.688062] 100000 sequences found
[0.825013] Done
[1.050532] Reading pre-graph file .//PreGraph
[1.050634] Graph has 7327 nodes and 100000 sequences
[1.064455] Scanning pre-graph file .//PreGraph for k-mers
[1.068171] 312686 kmers found
[1.118368] Sorting kmer occurence table ...
[1.206982] Sorting done.
[1.207082] Computing acceleration table...
[1.243785] Computing offsets...
[1.245568] Ghost Threading through reads 0 / 100000
[2.812996] === Ghost-Threaded in 1.567429 s
[2.813092] Threading through reads 0 / 100000
[4.160105] === Threaded in 1.347013 s
[4.163865] Correcting graph with cutoff 0.200000
[4.164097] Determining eligible starting points
[4.167082] Done listing starting nodes
[4.167124] Initializing todo lists
[4.167392] Done with initilization
[4.167425] Activating arc lookup table
[4.167616] Done activating arc lookup table
[4.169473] Concatenation...
[4.169666] Renumbering nodes
[4.169716] Initial node count 7327
[4.169824] Removed 15 null nodes
[4.169871] Concatenation over!
[4.169909] Clipping short tips off graph, drastic
[4.170925] Concatenation...
[4.171335] Renumbering nodes
[4.171390] Initial node count 7312
[4.171721] Removed 7144 null nodes
[4.171773] Concatenation over!
[4.171810] 168 nodes left
[4.171880] Writing into graph file .//Graph2...
[4.174911] Measuring median coverage depth...
[4.174995] Median coverage depth = 2.129032
[4.175049] Removing contigs with coverage < 1.064516...
[4.175097] Concatenation...
[4.175137] Renumbering nodes
[4.175173] Initial node count 168
[4.175204] Removed 0 null nodes
[4.175242] Concatenation over!
[4.175275] Concatenation...
[4.175307] Renumbering nodes
[4.175345] Initial node count 168
[4.175376] Removed 0 null nodes
[4.175406] Concatenation over!
[4.175442] Clipping short tips off graph, drastic
[4.175484] Concatenation...
[4.175516] Renumbering nodes
[4.175553] Initial node count 168
[4.175583] Removed 0 null nodes
[4.175613] Concatenation over!
[4.175654] 168 nodes left
[4.175691] Read coherency...
[4.175728] Identifying unique nodes
[4.175771] Done, 165 unique nodes counted
[4.175802] Trimming read tips
[4.175836] Renumbering nodes
[4.175868] Initial node count 168
[4.175898] Removed 0 null nodes
[4.175929] Confronted to 0 multiple hits and 0 null over 0
[4.175965] Read coherency over!
[4.176452] Starting pebble resolution...
[4.176922] Computing read to node mapping array sizes
[4.177126] Computing read to node mappings
[4.177201] Estimating library insert lengths...
[4.177671] Done
[4.177725] Computing direct node to node mappings
[4.177783] Scaffolding node 0
[4.177852] === Nodes Scaffolded in 0.000086 s
[4.177916] Preparing to correct graph with cutoff 0.200000
[4.178003] Cleaning memory
[4.178043] Deactivating local correction settings
[4.178084] Pebble done.
[4.178121] Concatenation...
[4.178162] Renumbering nodes
[4.178194] Initial node count 168
[4.178229] Removed 0 null nodes
[4.178266] Concatenation over!
[4.178305] Removing reference contigs with coverage < 1.064516...
[4.178354] Concatenation...
[4.178393] Renumbering nodes
[4.178431] Initial node count 168
[4.178469] Removed 0 null nodes
[4.178506] Concatenation over!
[4.178971] Writing contigs into .//contigs.fa...
[4.181588] Writing into stats file .//stats.txt...
[4.182090] Writing into graph file .//LastGraph...
[4.185227] Estimated Coverage = 2.129032
[4.185271] Estimated Coverage cutoff = 1.064516
Final graph has 168 nodes and n50 of 163, max 319, total 25832, using 832/100000 reads
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.fa
START-velveth
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velveth ./ 51 -fastq /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq ;
[0.000000] Reading FastQ file /home/studentx99/xprusa/cvic2/ws1/wgsim/out_paired_2000.er_0.05.1.fq;
[0.368783] 50000 sequences found
[0.368793] Done
[0.385298] Reading read set file .//Sequences;
[0.394986] 50000 sequences found
[0.450198] Done
[0.450283] 50000 sequences in total.
[0.450603] Writing into roadmap file .//Roadmaps...
[0.529267] Inputting sequences...
[0.529345] Inputting sequence 0 / 50000
[1.893678] === Sequences loaded in 1.364414 s
[1.893816] Done inputting sequences
[1.893820] Destroying splay table
[1.925613] Splay table destroyed
START-velvetg
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; ./velvetg ./ -exp_cov auto -ins_length 500
[0.000000] Reading roadmap file .//Roadmaps
[0.046371] 50000 roadmaps read
[0.046523] Creating insertion markers
[0.047278] Ordering insertion markers
[0.063958] Counting preNodes
[0.064388] 5143 preNodes counted, creating them now
[0.170240] Adjusting marker info...
[0.170296] Connecting preNodes
[0.171091] Cleaning up memory
[0.171095] Done creating preGraph
[0.171100] Concatenation...
[0.172340] Renumbering preNodes
[0.172344] Initial preNode count 5143
[0.172433] Destroyed 1825 preNodes
[0.172436] Concatenation over!
[0.172439] Clipping short tips off preGraph
[0.172992] Concatenation...
[0.173113] Renumbering preNodes
[0.173116] Initial preNode count 3318
[0.173131] Destroyed 2895 preNodes
[0.173134] Concatenation over!
[0.173135] 2786 tips cut off
[0.173137] 423 nodes left
[0.173166] Writing into pregraph file .//PreGraph...
[0.189466] Reading read set file .//Sequences;
[0.198956] 50000 sequences found
[0.299025] Done
[0.490776] Reading pre-graph file .//PreGraph
[0.503467] Graph has 423 nodes and 50000 sequences
[0.505130] Scanning pre-graph file .//PreGraph for k-mers
[0.505544] 55890 kmers found
[0.508030] Sorting kmer occurence table ...
[0.519620] Sorting done.
[0.535452] Computing acceleration table...
[0.561174] Computing offsets...
[0.561558] Ghost Threading through reads 0 / 50000
[1.232976] === Ghost-Threaded in 0.671418 s
[1.233051] Threading through reads 0 / 50000
[1.881018] === Threaded in 0.647967 s
[1.906652] Correcting graph with cutoff 0.200000
[1.906683] Determining eligible starting points
[1.906811] Done listing starting nodes
[1.906815] Initializing todo lists
[1.906825] Done with initilization
[1.906828] Activating arc lookup table
[1.906837] Done activating arc lookup table
[1.907104] Concatenation...
[1.907113] Renumbering nodes
[1.907116] Initial node count 423
[1.907121] Removed 3 null nodes
[1.907124] Concatenation over!
[1.907125] Clipping short tips off graph, drastic
[1.907167] Concatenation...
[1.907178] Renumbering nodes
[1.907181] Initial node count 420
[1.907188] Removed 26 null nodes
[1.907190] Concatenation over!
[1.907193] 394 nodes left
[1.907230] Writing into graph file .//Graph2...
[1.913595] Measuring median coverage depth...
[1.913670] Median coverage depth = 1.055970
[1.913685] Removing contigs with coverage < 0.527985...
[1.913698] Concatenation...
[1.913706] Renumbering nodes
[1.913709] Initial node count 394
[1.913711] Removed 0 null nodes
[1.913713] Concatenation over!
[1.913722] Concatenation...
[1.913729] Renumbering nodes
[1.913732] Initial node count 394
[1.913734] Removed 0 null nodes
[1.913736] Concatenation over!
[1.913738] Clipping short tips off graph, drastic
[1.913760] Concatenation...
[1.913767] Renumbering nodes
[1.913770] Initial node count 394
[1.913772] Removed 0 null nodes
[1.913775] Concatenation over!
[1.913777] 394 nodes left
[1.913779] Read coherency...
[1.913781] Identifying unique nodes
[1.913792] Done, 388 unique nodes counted
[1.913795] Trimming read tips
[1.913805] Renumbering nodes
[1.913808] Initial node count 394
[1.913810] Removed 0 null nodes
[1.913812] Confronted to 0 multiple hits and 0 null over 0
[1.913815] Read coherency over!
[1.914067] Starting pebble resolution...
[1.914307] Computing read to node mapping array sizes
[1.914406] Computing read to node mappings
[1.914435] Estimating library insert lengths...
[1.914664] Done
[1.914667] Computing direct node to node mappings
[1.914681] Scaffolding node 0
[1.914697] === Nodes Scaffolded in 0.000029 s
[1.914720] Preparing to correct graph with cutoff 0.200000
[1.914812] Cleaning memory
[1.914814] Deactivating local correction settings
[1.914820] Pebble done.
[1.914822] Concatenation...
[1.914828] Renumbering nodes
[1.914829] Initial node count 394
[1.914831] Removed 0 null nodes
[1.914834] Concatenation over!
[1.914836] Removing reference contigs with coverage < 0.527985...
[1.914850] Concatenation...
[1.914856] Renumbering nodes
[1.914857] Initial node count 394
[1.914859] Removed 0 null nodes
[1.914862] Concatenation over!
[1.915103] Writing contigs into .//contigs.fa...
[1.924744] Writing into stats file .//stats.txt...
[1.932421] Writing into graph file .//LastGraph...
[1.938797] Estimated Coverage = 1.055970
[1.951449] Estimated Coverage cutoff = 0.527985
Final graph has 394 nodes and n50 of 140, max 289, total 54856, using 892/50000 reads
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
START-assembly_stats
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
mv: cannot stat './contigs.fa': No such file or directory
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa.hist.log
382
264
251
240
252
260
283
252
225
246 =
287 =
268 =
269 =
226 =
258 =
246 =
240 =
243 =
268 =
242 ==
227 ==
229 ==
216 ==
250 ==
225 ==
211 ==
202 ==
208 ==
238 ==
26824 ===
98 ===
327 ===
312 ===
347 ===
286 ===
308 ===
286 ===
330 ===
303 ===
293 ====
280 ====
303 ====
290 ====
303 ====
265 ====
283 ====
324 ====
300 ====
273 ====
246 =====
283 =====
240 =====
265 =====
263 =====
283 =====
243 =====
291 =====
243 =====
244 =====
83444 ======
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
mv: cannot stat './contigs.fa': No such file or directory
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa.hist.log
382
264
251
240
252
260
283
252
225
246 =
287 =
268 =
269 =
226 =
258 =
246 =
240 =
243 =
268 =
242 ==
227 ==
229 ==
216 ==
250 ==
225 ==
211 ==
202 ==
208 ==
238 ==
26824 ===
98 ===
327 ===
312 ===
347 ===
286 ===
308 ===
286 ===
330 ===
303 ===
293 ====
280 ====
303 ====
290 ====
303 ====
265 ====
283 ====
324 ====
300 ====
273 ====
246 =====
283 =====
240 =====
265 =====
263 =====
283 =====
243 =====
291 =====
243 =====
244 =====
83444 ======
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa.hist.log
258
157
175
164
186
170
172
160
181
174 =
180 =
165 =
182 =
158 =
153 =
149 =
153 =
151 =
172 =
155 ==
164 ==
161 ==
154 ==
172 ==
159 ==
127 ==
130 ==
141 ==
160 ==
319 ===
76 ===
225 ===
189 ===
216 ===
200 ===
189 ===
208 ===
224 ===
209 ===
203 ====
164 ====
224 ====
197 ====
187 ====
183 ====
177 ====
195 ====
196 ====
174 ====
166 =====
193 =====
186 =====
168 =====
171 =====
179 =====
166 =====
163 =====
148 =====
180 =====
19917 ======
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
mv: cannot stat './contigs.fa': No such file or directory
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa.hist.log
1
7
2
3
2
3
7
4
10
2 =
1 =
2 =
2 =
1 =
2 =
2 =
2 =
4 ==
1 ==
5 ==
1 ==
3 ==
3 ==
2 ==
1 ===
1 ===
2 ===
4 ===
6 ===
7 ===
1 ===
2 ===
3 ===
2 ===
5 ====
1 ====
2 ====
4 ====
3 ====
3 ====
7 ====
3 ====
4 ====
3 ====
4 =====
3 =====
4 =====
2 =====
7 =====
4 =====
3 =====
2 =====
3 =====
484 ======
cd /home/studentx99/xprusa/cvic2/ws1/velvet ; mv ./contigs.fa ./contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
mv: cannot stat './contigs.fa': No such file or directory
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa.hist.log
1
7
2
3
2
3
7
4
10
2 =
1 =
2 =
2 =
1 =
2 =
2 =
2 =
4 ==
1 ==
5 ==
1 ==
3 ==
3 ==
2 ==
1 ===
1 ===
2 ===
4 ===
6 ===
7 ===
1 ===
2 ===
3 ===
2 ===
5 ====
1 ====
2 ====
4 ====
3 ====
3 ====
7 ====
3 ====
4 ====
3 ====
4 =====
3 =====
4 =====
2 =====
7 =====
4 =====
3 =====
2 =====
3 =====
484 ======
assembly_stats /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa
START-histogram-of-contig-lengths
cd /home/studentx99/xprusa/cvic2/ws1/velvet/ ; grep -v '>' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa ; awk '{ print "\t"length($0); }' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.fa | sort | uniq -c | sort -k2,2 -n > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa ; perl -lane 'print $F[0], "\t", "=" x ($F[1] / 10)' /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.contigs.data.len.fa > /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.hist.log ; cat /home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa.hist.log
5
7
7
3
7
9
3
7
13
5 =
5 =
4 =
4 =
5 =
3 =
2 =
5 =
2 =
1 ==
5 ==
3 ==
5 ==
5 ==
5 ==
2 ==
7 ==
6 ==
3 ===
3 ===
7 ===
11 ===
16 ===
12 ===
8 ===
9 ===
19 ===
9 ===
8 ====
8 ====
6 ====
15 ====
10 ====
9 ====
6 ====
11 ====
11 ====
7 ====
9 =====
7 =====
6 =====
5 =====
2 =====
6 =====
9 =====
7 =====
7 =====
5 =====
1031 ======
AR=( "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_31.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_31.out_paired_2000.er_0.05.1.fq.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_1.cv_51.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.fa" "/home/studentx99/xprusa/cvic2/ws1/velvet/contigs.c_8.cv_51.out_paired_2000.er_0.05.1.fq.fa" );
for i in ${AR[@]} ; do echo "F: $i"; assembly_stats $i > $i.ass.out; done
studentx99@hedron:~/xprusa/cvic2/ws1$
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