Pipeline does not complete variant calling when staring from the '--step prepare_recalibration'

[senzhaocode]

Description of the bug

Hello Sarek developer,

I am using Sarek pipeline (v3.0.1) to do somatic variant calling, and I started an analysis from '--step prepare_recalibration' using bam file after mark duplicates (e.g. *.md.bam); - see the command line in attached figure.

Pipeline was running normally and no errors were reported when it done, but it did not finish all steps (including variant calling) and there were no recalibrated bam files generated in output (e.g. *.recal.bam) as well. It looks the pipeline was terminated automatically after creating *.recal.table; - see attached log file.

I could not figure it out, and could you help me a troubleshooting.

Best

Sen

Command used and terminal output

No response

Relevant files

nextflow.log

System information

Nextflow version - 21.11.0
Hardware - HPC
Executor - slurm jobscript
Container engine - Singularity
OS - CentOS Linux
Version of nf-core/sarek - v3.0.1

[FriederikeHanssen]

can you provide the config + input file you used?

[FriederikeHanssen]

also did the pipeline terminate? what was the exit message?

[senzhaocode]

config file:
markduplicate.txt

input file:
markduplicates_no_table.csv
As the bam files (after MarkDuplicates) in the input sheet are private, I could not share with you now. Could you replace them with any testing data on your side. Thanks! I just would like to confirm that whether all steps in the pipeline will go through properly.

The terminate log message (it reported the pipeline completed successfully):

[senzhaocode]

BTW, in the output directory, no 'preprocessing' folder (which saves *.recal.bam) is available. I also screen the intermediate directory 'work' - there was *.recal.bam file of each genomic interval (recalibration processing should be work well), but they did not merge to a final *.recal.bam.

[FriederikeHanssen]

Hi! Just to double check: The log you posted says in the command it started from --step recalibrate and that it is version 3.0 . Is this the proper log for the problem above?

[FriederikeHanssen]

could finally reproduce this 🎉 one step closer to finding the issue

[varun171]

Hi Friederike,

I am having the same issue with sarek v3.1.2. Do you remember what was the issue and how was it resolved.

Thanks

Varun

nf-evObbXhThPAF9.log

[FriederikeHanssen]

Yes we fixed it in the code :D I can see in the log file, that Mutect2 is not spelled correctly, can you please try with --tools mutect2 instead?

[varun171]

Thanks. I will try and let you know.

On Tue, Mar 28, 2023 at 5:36 AM FriederikeHanssen ***@***.***> wrote: Yes we fixed it in the code :D I can see in the log file, that Mutect2 is not spelled correctly, can you please try with --tools mutect2 instead? — Reply to this email directly, view it on GitHub <#763 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABC763SMDT3OYASYEABD753W6KWI3ANCNFSM6AAAAAAQXTO64A> . You are receiving this because you commented.Message ID: ***@***.***>

-- Varun Kumar Kesherwani, PhD Senior Scientist

[juliawiggeshoff]

config file: markduplicate.txt

input file: markduplicates_no_table.csv As the bam files (after MarkDuplicates) in the input sheet are private, I could not share with you now. Could you replace them with any testing data on your side. Thanks! I just would like to confirm that whether all steps in the pipeline will go through properly.

The terminate log message (it reported the pipeline completed successfully):

was the issue here that the index file for the bams are saved as .bam.bam.bai? because sarek returns the error that this file does not exist, rightfully so. I have to remove the duplicated .bam and then it works. Using release 3.2.2.

Is this known and has it been fixed in recent releases?

[ltosti]

@FriederikeHanssen @maxulysse in Sarek 3.5.1 I get the same error; the pipeline completes "successfully" but actually stops after NFCORE_SAREK:SAREK:MULTIQC. When looking at the log, I can see this error:

DEBUG nextflow.util.HashBuilder - Unable to get file attributes file: s3://data/sample.bam.bai.bai -- Cause: java.nio.file.NoSuchFileException: s3://data/sample.bam.bai.bai

and this is how the first line of my samplesheet looks like:

patient,sex,status,sample,bam,bai
tum,XX,0,tum,s3://data/sample.bam,s3://data/sample.bam.bai

Any idea about which Sarek step is adding .bai twice? As the users above, I am using --step prepare_recalibration.

Thank you for your help!

[FriederikeHanssen]

Can yuo please post the log and full command?