Process `OptiType_RNA (test_sample)` terminated with an error exit status (1)

[DecodeGenome]

Dear nextNEOpi developers:

I use the HPC to run nextNEOpi test sample, I got the error below and I checked the rna_mapped_1.bam and rna_mapped_2.bam file are empty. Please help to identify and solve this issue.

Thank you very much in advance

############################################## Error messages ####################### Error executing process > 'OptiType_RNA (test_sample)'

Caused by: Process OptiType_RNA (test_sample) terminated with an error exit status (1)

Command executed:

OPTITYPE="$(readlink -f $(which OptiTypePipeline.py))" MHC_MAPPED_R1=$(samtools view -c rna_mapped_1.bam) MHC_MAPPED_R2=$(samtools view -c rna_mapped_2.bam) MHC_MAPPED=$((MHC_MAPPED_R1+MHC_MAPPED_R2)) if [ "$MHC_MAPPED" != "0" ]; then $OPTITYPE -i rna_mapped_1.bam rna_mapped_2.bam -e 1 -b 0.009 --rna -o ./tmp && \ mv ./tmp//_result.tsv ./test_sample_optitype_RNA_result.tsv && \ mv ./tmp//_coverage_plot.pdf ./test_sample_optitype_RNA_coverage_plot.pdf && \ rm -rf ./tmp/ else touch test_sample_optitype_RNA_result.tsv echo "No result" > test_sample_optitype_RNA_coverage_plot.pdf fi

Command exit status: 1

Command output: (empty)

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred [main_samview] fail to read the header from "rna_mapped_1.bam".

Work dir: /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/10/dd9392940df5469d3ed8ef2b821f25

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[riederd]

Hi, can you provide the contents of /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/10/dd9392940df5469d3ed8ef2b821f25 as tar.gz file? as well as the .nextflow.log

Thanks

[DecodeGenome]

Dear Dr. Dietmar,

Thanks you very much for your prompt response. Please find files you need which could help you identify the problems.

Beste Regards,

Wei

---

From: Dietmar Rieder @.> Sent: Thursday, April 25, 2024 1:16 AM To: icbi-lab/nextNEOpi @.> Cc: Wu, Wei @.>; Author @.> Subject: Re: [icbi-lab/nextNEOpi] Process OptiType_RNA (test_sample) terminated with an error exit status (1) (Issue #73)

Hi, can you provide the contents of /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/10/dd9392940df5469d3ed8ef2b821f25 as tar. gz file? as well as the .nextflow. log Thanks — Reply to this email directly, view it on GitHub, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd

Hi, can you provide the contents of /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/10/dd9392940df5469d3ed8ef2b821f25 as tar.gz file? as well as the .nextflow.log

Thanks

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/icbi-lab/nextNEOpi/issues/73*issuecomment-2076626795__;Iw!!LQC6Cpwp!rmwI7HcEzpBlJ2JQy_2uVLKwC-IqnHbLPFNF9fR5_MlNoRkazN6PXPfivUHjh3gBq0LJ0Yww20EBejdjpm5q_kZn$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ADZWCCB6G5XMWBAQ3DSMACDY7C3U3AVCNFSM6AAAAABGYAN2C2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZWGYZDMNZZGU__;!!LQC6Cpwp!rmwI7HcEzpBlJ2JQy_2uVLKwC-IqnHbLPFNF9fR5_MlNoRkazN6PXPfivUHjh3gBq0LJ0Yww20EBejdjpsVfXQPB$. You are receiving this because you authored the thread.Message ID: @.***>

[riederd]

Unfortunately I cannot see any files.

[DecodeGenome]

Hi Riederd,

The files are attached here now, please let me know whether you can see them.

Thanks, Wei

contents.tar.gz nextflow.log

[riederd]

it seems that the bam files created in teh pre_map_hla_RNA are invalid: /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/9e/57ee15ac58f72351d24ddb25b46813/rna_mapped_1.bam /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/9e/57ee15ac58f72351d24ddb25b46813/rna_mapped_2.bam

what are the contents of that directory?

[DecodeGenome]

Hi, Riederd, here is the contents in /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/9e/57ee15ac58f72351d24ddb25b46813/

Thanks,

9e_contents.tar.gz

[riederd]

There seems to be a problem with creating temporary files on your system in the /scratch dir: the .command.err from the 9e contents says:

Couldn't create temporary file /scratch/wwu888/SQN38WCAC. (No such file or directory)
/home/mi/dadi/workspace/development/seqan/include/seqan/file/string_mmap.h:635 FAILED!  (Memory Mapped String couldn't open temporary file)

[DecodeGenome]

Hi Riederd, We defined "tmpDir: /wynton/scratch/wwu888/nextNEOpi" (see in nextflow.log, line="Apr-24 21:11:40.257 [main] INFO nextflow.script.BaseScript") , why the nextNeopi is trying to create temporay file to "/scratch/wwu888/" here. Even using this directory, I checked the directory "scratch/wwu888", it has sufficient memory there. How to ask the pipeline to use tmpDir:/wynton/scratch/wwu888/nextNEOpi?

Thanks,

[riederd]

Hi, it is not nextNEOpi directly trying to write into /scratch/wwu888 it is the yara_mapper which reads the ENV variable $TEMPDIR and uses that value to write temporary files. I guess you have /scratch/wwu888 set as $TEMPDIR on your system, however this is not mounted into the singularity container that runs the yara_mapper.

So one thing you could try is to set $TEMPDIR to the same directory you are using as tmpDir in nextNEOpi before launching the pipeline, i.e.: $ export TEMPDIR=/wynton/scratch/wwu888/nextNEOpi

[DecodeGenome]

Hi Riederd, I tried your suggestion, it is the same error. yara_mapper still reads the ENV as /scratch/wwu888. I checked /scratch/wwu888, it does contain singularity. Any other sugguestions?

Thanks, Wei

[DecodeGenome]

Hi, The problem was solved with setting: "export SINGULARITYENV_TMPDIR=/wynton/scratch/wwu888/nextNEOpi". However, when running the command: a new error occured, see #17.

Thanks,

Wei

[riederd]

Can you provide more details

[riederd]

Closing: no more details provided. Please check if v1.4.1 is fixing this.