Having an issue running GeneMark, within Braker.
Versions
perl /share/braker.pl --version
braker.pl version 1.6
perl /share/gm_et_linux_64/gmes_petap/gmes_petap.pl
# -------------------
Usage: /share/gm_et_linux_64/gmes_petap/gmes_petap.pl [options] --sequence [filename]
GeneMark-ES Suite version 4.30
includes transcript (GeneMark-ET) and protein (GeneMark-EP) based training and prediction
Running BRAKER:
perl /share/braker.pl \
--genome ../genome/Mya.genome.v1.1.1.fasta \
--bam ../genome/transcriptome.clam.v.1.11.bam \
--BAMTOOLS_PATH=/share/bamtools/bin/ \
--UTR on --cores 10 --species=Mya_a
perl /share/braker.pl --genome ../genome/Mya.genome.v1.1.1.fasta --bam ../genome/transcriptome.clam.v.1.11.bam --BAMTOOLS_PATH=/share/bamtools/bin/ --UTR on --cores 10 --species=Mya_a
NEXT STEP: check files and settings
NEXT STEP: check options
... options check complete.
NEXT STEP: check fasta headers
fasta headers check complete.
NEXT STEP: create SAM header file /mouse/Mya/maker/braker/Mya_a/transcriptome_header.sam.
SAM file /mouse/Mya/maker/braker/Mya_a/transcriptome_header.sam complete.
NEXT STEP: check BAM headers
headers check for BAM file /mouse/Mya/maker/../genome/transcriptome.clam.v.1.11.bam complete.
NEXT STEP: make hints from BAM file /mouse/Mya/maker/../genome/transcriptome.clam.v.1.11.bam
Wait a moment, calculating maximum block size that needs to be allocated... .. done
hints from BAM file /mouse/Mya/maker/../genome/transcriptome.clam.v.1.11.bam added.
NEXT STEP: sort hints
hints sorted.
NEXT STEP: summarize multiple identical hints to one
hints joined.
NEXT STEP: filter introns, find strand and change score to 'mult' entry
strands found and score changed.
hints file complete.
NEXT STEP: execute GeneMark-ET
failed to execute: perl /share/gm_et_linux_64/gmes_petap//gmes_petap.pl --sequence=/mouse/Mya/maker/braker/Mya_a/genome.fa --ET=/mouse/Mya/maker/braker/Mya_a/hintsfile.gff --cores=10 1>/mouse/Mya/maker/braker/Mya_a/GeneMark-ET
.stdout 2>/mouse/Mya/maker/braker/Mya_a/errors/GeneMark-ET.stderr
The stderr and stdout are empty
here is gmes.log
more gmes.log
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:52:40 2015] /share/gm_et_linux_64/gmes_petap/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/d
na.trace --in /mouse/Mya/maker/braker/Mya/genome.fa
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:52:41 2015] /share/gm_et_linux_64/gmes_petap/reformat_gff.pl --out data/et.gff --trace info/dna.trace --in /mouse/Mya/maker/braker/Mya/hintsfile.gff --quiet
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:53:54 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/dna.fna --allow_x --stat info/dna.general
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:55:11 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:55:46 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:57:23 2015] /share/gm_et_linux_64/gmes_petap/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:58:38 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq /mouse/Mya/maker/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 50000 --letters_per
_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.trace
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:59:05 2015] /share/gm_et_linux_64/gmes_petap/rescale_gff.pl --in data/et.gff --trace info/training.trace --out data/et_training.gff
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:59:22 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:59:26 2015] /share/gm_et_linux_64/gmes_petap/parse_by_introns.pl --section ET_ini --cfg /mouse/Mya/maker/run.cfg --parse_dir /mouse/Mya/maker/run/ET_ini
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:59:27 2015] /share/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /mouse/Mya/maker/run.cfg --section donor_GT --format DONOR
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 08:59:27 2015] error
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:06:36 2015] /share/gm_et_linux_64/gmes_petap/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/d
na.trace --in /mouse/Mya/maker/braker/Mya/genome.fa
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:06:37 2015] /share/gm_et_linux_64/gmes_petap/reformat_gff.pl --out data/et.gff --trace info/dna.trace --in /mouse/Mya/maker/braker/Mya/hintsfile.gff --quiet
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:07:45 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/dna.fna --allow_x --stat info/dna.general
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:09:06 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:09:37 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:11:08 2015] /share/gm_et_linux_64/gmes_petap/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:12:23 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq /mouse/Mya/maker/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 50000 --letters_per
_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.trace
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:12:51 2015] /share/gm_et_linux_64/gmes_petap/rescale_gff.pl --in data/et.gff --trace info/training.trace --out data/et_training.gff
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:13:07 2015] /share/gm_et_linux_64/gmes_petap/probuild --seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:13:12 2015] /share/gm_et_linux_64/gmes_petap/parse_by_introns.pl --section ET_ini --cfg /mouse/Mya/maker/run.cfg --parse_dir /mouse/Mya/maker/run/ET_ini
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:13:12 2015] /share/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /mouse/Mya/maker/run.cfg --section donor_GT --format DONOR
/share/gm_et_linux_64/gmes_petap//gmes_petap.pl : [Mon Oct 5 09:13:12 2015] error
looks like the last command has failed: /share/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /mouse/Mya/maker/run.cfg --section donor_GT --format DONOR
/share/gm_et_linux_64/gmes_petap/make_nt_freq_mat.pl --cfg /mouse/Mya/maker/run.cfg --section donor_GT --format DONOR
error, no valid sequences were found
from the cfg
file
donor_GT:
auto_order: 1
format_out: ''
gc_high: -1
gc_low: -1
infile: /mouse/Mya/maker/braker/Mya_a/GeneMark-ET/run/ET_ini/don.seq
margin: 3
order: 0
outfile: GT.mat
phase: ''
pseudocounts: 10
quite: 0
site_size: 2
threshold_zero: 2000
type: GT
width: 9
Of note, in the cfg
file originally it had listed don.seq
with no path - and I was getting file not found
errors related to that file. I see that don.seq
is located elsewhere, so I changed the config file accordingly. However, /mouse/Mya/maker/braker/Mya_a/GeneMark-ET/run/ET_ini/don.seq
is empty so the erro rmust be more upstream.
Any help greatly appreciated.
Hi! I just found this rather randomly when I ran into the above "inappropriate ioctl for device" problem, here's how I fixed that particular problem for me.
I checked braker.log in the output folder which revealed that the last command it tried to run was this one:
Running that command manually revealed that Braker1 was throwing an error message away:
So what happened (for me) is that in re-compiling bam2hints I messed up and gave it the wrong path to bamtools' libbamtools.a but for some crazy reason it still compiled. Recompiling bam2hints with the proper LIBS path as described in the bam2hints README then worked, as in:
After that the annoying "inappropriate ioctl for device" disappeared.