inchworm error

[Shoyo Sato]

Hello!

I'm running trinity on multiple samples with an array job and I seem to be having issues with inchworm in one sample. It works perfectly for all others. I used the --no_bowtie flag as recommended in previous threads and that fixed the issue.

It's my understanding that trinity uses bowtie to link alternatively spliced isoforms to the more complete isoforms. Does this mean all of the alternative transcripts will only be partial because I skipped bowtie?

I would also like to know what it is about this dataset that is problematic. The fastqc reports are not perfect but I've assembled worse datasets.

Some more details about the run:

Data are from SRA (SRR1232833, SRR1232821)

~6 million read pairs after rcorrect, trimg, and bowtie filtering for rRNA so I think 50G is plenty of memory.

Using trinity v2.15.1 on singularity. The trinity command:

Trinity --max_memory 50G --CPU 12 --output trinity/TEMP_trinity --seqType fq --SS_lib_type FR --full_cleanup \ --left bowtie/*Cleaned.1.fq --right bowtie/*Cleaned.2.fq \ --path_reinforcement_distance 75 --bflyHeapSpaceMax 10G --bflyCalculateCPU

The error message:

Error encountered::  <!----
CMD: /usr/local/bin/util/support_scripts/scaffold_iworm_contigs.pl /home/projects/ku_00156/scratch/ssato/transcriptome_assembly_test/assembly_prep/Marphysa_bellii/trinity/TEMP_trinity/chrysalis/iworm.bowtie.nameSorted.bam /home/projects/ku_00156/scratch/ssato/transcriptome_assembly_test/assembly_prep/Marphysa_bellii/trinity/TEMP_trinity/chrysalis/inchworm.fa.min100 > /home/projects/ku_00156/scratch/ssato/transcriptome_assembly_test/assembly_prep/Marphysa_bellii/trinity/TEMP_trinity/chrysalis/iworm_scaffolds.txt 2>tmp.19822.1710943389.stderr

Errmsg:
Killed

--->

Error, cmd: /usr/local/bin/util/support_scripts/scaffold_iworm_contigs.pl /home/projects/ku_00156/scratch/ssato/transcriptome_assembly_test/assembly_prep/Marphysa_bellii/trinity/TEMP_trinity/chrysalis/iworm.bowtie.nameSorted.bam /home/projects/ku_00156/scratch/ssato/transcriptome_assembly_test/assembly_prep/Marphysa_bellii/trinity/TEMP_trinity/chrysalis/inchworm.fa.min100 > /home/projects/ku_00156/scratch/ssato/transcriptome_assembly_test/assembly_prep/Marphysa_bellii/trinity/TEMP_trinity/chrysalis/iworm_scaffolds.txt 2>tmp.19822.1710943389.stderr died with ret 35072  at /usr/local/bin/PerlLib/Pipeliner.pm line 187.
Pipeliner::run(Pipeliner=HASH(0x555555f14ec8)) called at /usr/local/bin/Trinity line 2124
main::run_chrysalis("/home/projects/ku_00156/scratch/ssato/transcriptome_assembly_"..., "/home/projects/ku_00156/scratch/ssato/transcriptome_assembly_"..., 200, 500, "FR", "/home/projects/ku_00156/scratch/ssato/transcriptome_assembly_"..., "/home/projects/ku_00156/scratch/ssato/transcriptome_assembly_"...) called at /usr/local/bin/Trinity line 1895
main::run_Trinity() called at /usr/local/bin/Trinity line 1500
eval {...} called at /usr/local/bin/Trinity line 1499

Trinity run failed. Must investigate error above.

Thank you for your help!

Best,

Shoyo