peterdfields

This is WhatsHap (polyploid) 1.8.dev47+g7ea2349.d20230412 running under Python 3.10.10
======== Working on chromosome '3GT_maker_scaffold_1335_augustus_gene_0.3_mRNA_1_tr'
---- Processing individual sample
Number of variants skipped due to missing genotypes: 0
Number of remaining heterozygous variants: 107
Found 1258 reads covering 107 variants
Kept 1210 reads that cover at least two variants each
Detecting connected components with weak interconnect ..
Split heterozygous variants into 1 blocks (and 0 singleton blocks).
Phasing block 1 of 1 with 1210 reads and 107 variants.

peterdfields

=== ROCm TechSupport Log Collection Utility: V1.36 ===
Sat Jan  7 09:59:37 PM EST 2023
===== Section: OS Distribution         ===============
Linux fisher 5.15.0-56-generic #62-Ubuntu SMP Tue Nov 22 19:54:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
PRETTY_NAME="Ubuntu 22.04.1 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.1 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu

peterdfields

/home/peter/bioinformatics/LJA/bin/lja -t 10 -o lja_base --reads demultiplex.bc1001_BAK8A_OA--bc1001_BAK8A_OA.hifi_reads.fasta.gz 
00:00:00 2Mb  INFO: Hello. You are running La Jolla Assembler (LJA), a tool for genome assembly from PacBio HiFi reads
00:00:00 5Mb  TRACE: Git diff:
00:00:00 5Mb  INFO: LJA pipeline started
00:00:00 5Mb  INFO: Performing initial correction with k = 501
00:00:00 0Mb  INFO: Reading reads
00:00:00 0Mb  INFO: Extracting minimizers
00:00:00 2Mb  TRACE: Starting parallel calculation using 10 threads
00:00:10 1.1Gb  TRACE: 105250 items of total length 1073745299 processed 
00:00:20 2.2Gb  TRACE: 103293 items of total length 1073746126 processed 

peterdfields

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

Apr 26 16:18:48 ...... FATAL ERROR, exiting

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

Apr 26 20:43:28 ...... FATAL ERROR, exiting

EXITING: Did not find the genome in memory, did not remove any genomes from shared memory

peterdfields

# Command to run bwa mem to remap reads from a position sorted bam file to new reference and output a position sorted bam file.
# You need the following tools available in your PATH variable in order for this command to work without using absolute paths
# 1. samtools
# 2. bwa
# You will need to have generated an index for the new reference using 'bwa index' for this command to work.
# Additional variables to keep in mind which are labeled X, Y, and Z in the command (these values need to be replaced by a integer representing resources available for individual steps; note that 'tmpxyz' is not a variable but an actual value to be used in the command)
# Generally my impression is that these steps are executed in sequence rather than simultaneously but there is probably some overlap in which case take care that excess resources aren't demanded of the machine/resource you're using
# X is the number of CPUs that can be used for the bwa mem mapping step
# Y is the number of threads to be used for the conversion of sa

peterdfields

Possible precedence issue with control flow operator at /home/peter/miniconda3/envs/annotation/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Codon table 1 in use. You can change it using --table option.
Use of uninitialized value in concatenation (.) or string at /home/peter/miniconda3/envs/annotation/bin/agat_sp_fix_longest_ORF.pl line 1047.
Use of uninitialized value in concatenation (.) or string at /home/peter/miniconda3/envs/annotation/bin/agat_sp_fix_longest_ORF.pl line 1047.
Use of uninitialized value in concatenation (.) or string at /home/peter/miniconda3/envs/annotation/bin/agat_sp_fix_longest_ORF.pl line 1047.
Use of uninitialized value in concatenation (.) or string at /home/peter/miniconda3/envs/annotation/bin/agat_sp_fix_longest_ORF.pl line 1047.
Use of uninitialized value in concatenation (.) or string at /home/peter/miniconda3/envs/annotation/bin/agat_sp_fix_longest_ORF.pl line 1047.
Use of uninitialized value in concatenation (.) or string at /home/peter/miniconda3/envs/annotation/bin/

peterdfields

--------------------------------------------------------------------------
pyPaSWAS run started at: 2018-12-25 16:45:43 using the following settings:
--------------------------------------------------------------------------
mismatch_score                :                            -4
device_number                 :                             0
relative_score                :                          0.01
query_coverage_slice          :                          0.98
filter_factor                 :                          0.01
device_type                   :                           GPU

peterdfields

[UNITIGGING/READS]
--
-- In sequence store './pest_update_assemble.seqStore':
--   Found 1779192 reads.
--   Found 5583887414 bases (11.16 times coverage).
--
--   Read length histogram (one '*' equals 12404.67 reads):
--     1000   1999 868327 **********************************************************************
--     2000   2999 324401 **************************
--     3000   3999 192553 ***************

peterdfields

[TRIMMING/READS]
--
-- In sequence store './pest_update_trim.seqStore':
--   Found 6124543 reads.
--   Found 35228747202 bases (70.45 times coverage).
--
--   Read length histogram (one '*' equals 21794.92 reads):
--     1000   1999 1525645 **********************************************************************
--     2000   2999 958107 *******************************************
--     3000   3999 647409 *****************************

peterdfields

[CORRECTION/READS]
--
-- In sequence store './pest_update2trim.seqStore':
--   Found 6377809 reads.
--   Found 37174774356 bases (74.34 times coverage).
--
--   Read length histogram (one '*' equals 53255.4 reads):
--        0   4999 3727878 **********************************************************************
--     5000   9999 1519983 ****************************
--    10000  14999 670858 ************