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Hello, I am very grateful for your development of the Sarek pipeline. This pipeline has been very helpful to me in handling WGS analysis. However, I encountered an error when testing the pipeline with the test dataset. I would like to ask what might have caused this error.
When I provide a pair of normal and tumor data, an error occurs when calling BAM_VARIANT_CALLING_SOMATIC_ALL in the variant_calling step. The error message is as follows:
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP (1)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP` input file name collision -- There are multiple input files for each of the following file names: HCC1395T_vs_HCC1395N.mpileup.gz
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Description of the bug
Hello, I am very grateful for your development of the Sarek pipeline. This pipeline has been very helpful to me in handling WGS analysis. However, I encountered an error when testing the pipeline with the test dataset. I would like to ask what might have caused this error.
When I provide a pair of normal and tumor data, an error occurs when calling BAM_VARIANT_CALLING_SOMATIC_ALL in the variant_calling step. The error message is as follows:
And this is the sample.stomatic.csv:
This is the configuration file that I set up, with other parameters kept at default values:
Could you please provide valuable suggestions for this runtime error? Thank you very much!
Command used and terminal output
nextflow run ${nfcorePath}/nf-core-sarek_3.4.0/3_4_0 -profile singularity -c wes.conf --outdir ./outdir --genome GATK.GRCh38
Relevant files
nextflow.log
System information
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