variant_calling DO NOT PROCESS

torres-HI commented 2 months ago

Description of the bug

Hi am working with the pipeline, in the test working fine. with samples do not report the VARIANT_CALLING, there is no error in the run. How I can make that processes?

Command used and terminal output

nf-core/sarek v3.4.4-g5cc3049
------------------------------------------------------
Core Nextflow options
  revision             : 3.4.4
  runName              : maniac_pasteur
  containerEngine      : singularity
  launchDir            : /mnt/lustre/koa/scratch/torres91/mw
  workDir              : /mnt/lustre/koa/scratch/torres91/mw/work
  projectDir           : /home/torres91/.nextflow/assets/nf-core/sarek
  userName             : torres91
  profile              : singularity
  configFiles          : 

Input/output options
  input                : samplesheet.csv
  outdir               : /home/torres91/koa_scratch/mw/tes_results

Main options
  intervals            : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed

Reference genome options
  genome               : GRCm38
  bwa                  : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/
  chr_dir              : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes
  dbsnp                : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz
  dbsnp_tbi            : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi
  dict                 : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict
  fasta                : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa
  fasta_fai            : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai
  known_indels         : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz
  known_indels_tbi     : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi
  mappability          : s3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem
  snpeff_db            : 99
  snpeff_genome        : GRCm38
  vep_genome           : GRCm38
  vep_species          : mus_musculus
  vep_cache_version    : 102
  save_reference       : true

.
.
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Plus 13 more processes waiting for tasks…
-[nf-core/sarek] Pipeline completed successfully-
Completed at: 11-Sep-2024 22:40:04
Duration    : 3h 18m 27s
CPU hours   : 49.6 (0% cached)
Succeeded   : 233
Cached      : 20

Relevant files

ls -lth tes_results total 1488 drwxr-x--- 6 alikam staff 192B Sep 11 17:19 preprocessing drwxr-x--- 8 alikam staff 256B Sep 11 17:12 reports drwxr-x--- 4 alikam staff 128B Sep 11 17:07 reference drwxr-x--- 18 alikam staff 576B Sep 11 12:40 pipeline_info -rw-r-----@ 1 alikam staff 635K Sep 11 12:40 sarek_3528528_4294967294_error.out drwxr-x--- 5 alikam staff 160B Sep 11 12:37 multiqc drwxr-x--- 5 alikam staff 160B Sep 11 12:37 csv -rw-r----- 1 alikam staff 826B Sep 11 09:19 samplesheet.csv

System information

No response

asp8200 commented 2 months ago

What variant-callers did you select? You can select the variant-callers you want to use by using the option --tools in your nextflow command, like, for instance, --tools freebayes,strelka.

The tools can, of course, also be specified in a config-file.

torres-HI commented 2 months ago

Thanks, I'll check them out.

On Wed, Sep 11, 2024 at 7:27 PM Anders Sune Pedersen < @.***> wrote:

What variant-callers did you select? You can select the variant-callers you want to use by using the option --tools in your nextflow command, like, for install, --tools freebayes,strelka.

The tools can, of course, also be specified in a config-file.

— Reply to this email directly, view it on GitHub https://github.com/nf-core/sarek/issues/1648#issuecomment-2345303369, or unsubscribe https://github.com/notifications/unsubscribe-auth/BKWED2ER6Q33XLJKTFUJ3GLZWEQ3PAVCNFSM6AAAAABOCIM5AGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBVGMYDGMZWHE . You are receiving this because you authored the thread.Message ID: @.***>

nf-core / sarek