Process pipeline:differential_expression:count_transcripts (1) terminated with an error exit status (1)

[BenjaminBajzelj]

Ask away!

Hi!

I get an error in the log file:

executor > local (24)
[bd/f84e36] process > validate_sample_sheet [100%] 1 of 1, cached: 1 ✔
[d7/72c478] process > fastcat (10) [100%] 22 of 22, cached:...
[bf/9dca9d] process > pipeline:preprocess_ref_ann... [100%] 1 of 1, cached: 1 ✔
[db/c87895] process > pipeline:collectFastqIngres... [100%] 22 of 22, cached:...
[5b/af531c] process > pipeline:getVersions [100%] 1 of 1, cached: 1 ✔
[99/177a19] process > pipeline:getParams [100%] 1 of 1, cached: 1 ✔
[f7/3cef66] process > pipeline:preprocess_reads (22) [ 0%] 0 of 22
[ee/97659e] process > pipeline:check_annotation_s... [100%] 1 of 1, cached: 1 ✔
[0e/f0893a] process > pipeline:preprocess_ref_tra... [100%] 1 of 1, cached: 1 ✔
[fa/9bcdb0] process > pipeline:differential_expre... [100%] 1 of 1, cached: 1 ✔
[b7/554a16] process > pipeline:differential_expre... [100%] 1 of 1, cached: 1 ✔
[00/18628f] process > pipeline:differential_expre... [ 4%] 1 of 22, cached: 1
[7d/6e395f] process > pipeline:differential_expre... [ 0%] 0 of 1
[- ] process > pipeline:differential_expre... -
[- ] process > pipeline:differential_expre... -
[- ] process > pipeline:differential_expre... -
[- ] process > pipeline:differential_expre... -
[- ] process > pipeline:makeReport -
[- ] process > output -
WARN: Input directory 'barcode18' was found, but sample sheet 'linear_mRNA.csv' has no such entry.
WARN: Input directory 'barcode17' was found, but sample sheet 'linear_mRNA.csv' has no such entry.
ERROR ~ Error executing process > 'pipeline:differential_expression:count_transcripts (1)'

Caused by:
Process pipeline:differential_expression:count_transcripts (1) terminated with an error exit status (1)

Command executed:

salmon quant --noErrorModel -p "4" -t "amended.ref_transcriptome" -l SF -a "1004N_reads_aln_sorted.bam" -o counts
mv counts/quant.sf "1004N.transcript_counts.tsv"
seqkit bam "1004N_reads_aln_sorted.bam" 2> "1004N.seqkit.stats"

Command exit status:
1

Command output:
(empty)

Command error:
Version Info: ### PLEASE UPGRADE SALMON ###

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The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.

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salmon (alignment-based) v1.9.0

[ program ] => salmon

[ command ] => quant

[ noErrorModel ] => { }

[ threads ] => { 4 }

[ targets ] => { amended.ref_transcriptome }

[ libType ] => { SF }

[ alignments ] => { 1004N_reads_aln_sorted.bam }

[ output ] => { counts }

Logs will be written to counts/logs
[2024-09-27 11:38:48.747] [jointLog] [info] setting maxHashResizeThreads to 4
[2024-09-27 11:38:48.747] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
Library format { type:single end, relative orientation:none, strandedness:sense }
[2024-09-27 11:38:48.748] [jointLog] [info] numQuantThreads = 2
parseThreads = 2
Checking that provided alignment files have consistent headers . . . done
Populating targets from aln = "1004N_reads_aln_sorted.bam", fasta = "amended.ref_transcriptome" . . .done

[2024-09-27 11:38:50.774] [jointLog] [info] replaced 0 non-ACGT nucleotides with random nucleotides

killing thread 0 . . . done

killing thread 1 . . . done

[2024-09-27 11:39:01.051] [jointLog] [warning] salmon was only able to assign 0 fragments to transcripts in the index, but the minimum number of required assigned fragments (--minAssignedFrags) was 10. This could be indicative of a mismatch between the reference and sample, or a very bad sample. You can change the --minAssignedFrags parameter to force salmon to quantify with fewer assigned fragments (must have at least 1).

Work dir:
/ceph/hpc/data/s24o01-29-users/Nextflow/work/7d/6e395fda85d46ca1cc1e350253de34

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details

The command that gives the error is:

#!/bin/bash -euo pipefail
salmon quant --noErrorModel -p "4" -t "amended.ref_transcriptome" -l SF -a "1004N_reads_aln_sorted.bam" -o counts
mv counts/quant.sf "1004N.transcript_counts.tsv"
seqkit bam "1004N_reads_aln_sorted.bam" 2> "1004N.seqkit.stats"

where amended.ref_transcriptome's size is around 0,5 gigabytes and 1004N_reads_aln_sorted.bam's size around 2,5 gigabytes (they are not empty). I have NO paired-end or strand-specific reads, but it says in the workflow that argument -SF should be used anyhow because pychopper was used in that case.

Now I don't know exactly where the problem is?

[sarahjeeeze]

Hi, would you mind sharing either your 'nextflow.log' file and/or your full input cmd - also confirm if you are inputting rna or cdna