FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX is launched multiple times and fails #1003
Comments
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Hi, Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa)'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX (genome.transcripts.fa)` terminated with an error exit status (1)
Command executed:
grep '^>' genome.fa | cut -d ' ' -f 1 | cut -d $'\t' -f 1 > decoys.txt
sed -i.bak -e 's/>//g' decoys.txt
cat genome.transcripts.fa genome.fa > gentrome.fa
salmon \
index \
--threads 6 \
-t gentrome.fa \
-d decoys.txt \
\
-i salmon
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX":
salmon: $(echo $(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Version Server Response: Not Found
index ["salmon"] did not previously exist . . . creating it
[2023-04-21 08:14:02.228] [jLog] [info] building index
out : salmon
[2023-04-21 08:14:02.231] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2023-04-21 08:14:13.976] [puff::index::jointLog] [warning] Entry with header [rna74458], had length less than equal to the k-mer length of 31 (perhaps after poly-A clipping)
[2023-04-21 08:14:14.653] [puff::index::jointLog] [warning] Removed 150 transcripts that were sequence duplicates of indexed transcripts.
[2023-04-21 08:14:14.653] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag
[2023-04-21 08:14:14.653] [puff::index::jointLog] [critical] The decoy file contained the names of 195 decoy sequences, but 0 were matched by sequences in the reference file provided. To prevent unintentional errors downstream, please ensure that the decoy file exactly matches with the fasta file that is being indexed.
[2023-04-21 08:14:14.690] [puff::index::jointLog] [error] The fixFasta phase failed with exit code 1
Work dir:
/home/emmanuel/pepkon/work/3a/4f6c3e84cc6753389d3f9d1c88c136
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Here are the command that I use : |
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Same issue, sometime with exit code 1 and sometimes 137. Hard to pinpoint what error even is, only things I see in .command.err and .command.log are what I assume to be unrelated warnings: |
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The problem lies in the invocation of the FASTQ_SUBSAMPLE_FQ_SALMON subworkflow. It is expecting to be provided with a value channel, but instead we provide a queue channel. This is fixed with #1006 by passing the ch_genome_fasta channel through the The fix above is made directly to the rnaseq workflow, but that does not preclude modifications to the subworkflow to make it a little bit more defensive. |
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Thanks for reporting @JohannesKersting @lextallan @EmmanuelLabaronne and for the fix @robsyme ! #1006 has been merged into |
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Hi, thank you all ! |
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Great! |
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Hi all, I am commenting on this, as I am now facing the same issue, but with nf-core rnaseq pipeline version 3.14.0 Here the output I get:`[88/310ad2] NFC…OME:GTF_FILTER (genome.fa) | 1 of 1 ✔ Caused by: Command executed: grep '^>' genome.fa | cut -d ' ' -f 1 | cut -d $'\t' -f 1 > decoys.txt salmon cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -[nf-core/rnaseq] Pipeline completed with errors- or in short, the crucial part:
Used command: other information:
I am honestly quite new to nf-core, and would appreciate some guidance on what to do now. For example, I read all of the information before but I honestly would not entirely understand how to change my used command based on the information from @robsyme (nothing to do with you, but with me and my currently still limiting knowledge!). Thanks so much for the help. |
Description of the bug
As can be seen in the screenshot down below, the pipeline lists and executes the task FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX six times, which is the number of samples in the sample sheet used. The pipeline fails in the same step. Additionally, some instances of the task are not cleared from the slurm queue after the pipeline fails.
Running everything with -r 3.10.1 works and FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX runs only once.
Command used and terminal output
Relevant files
relevant_files.zip
System information
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