Closed jurummel closed 1 month ago
Hi Julian,
thanks for reporting this issue.
It looks like the N-masked fasta file required for the bowtie index is missing. It should have been generated in the previous step. Did rule create_snpgenome
produce any errors?
Best,
Katarzyna
Hi Katarzyna,
thanks for the quick reply. I don't get an error message for rule create_snpgenome
.
rule create_snpgenome:
input: /projects/allelespecificchromatinmouse/work/MouseSeqData/Indices_Mapping/genome_fasta
output: snp_genome/CAST_EiJ_SNP_filtering_report.txt, snp_genome/C57BL_6NJ_SNP_filtering_report.txt, snp_genome/CAST_EiJ_C57BL_6NJ_dual_hybrid.based_on_GRCm38_105_Mapping_N-masked, snp_genome/all_C57BL_6NJ_SNPs_CAST_EiJ_reference.based_on_GRCm38_105_Mapping.txt
log: SNPsplit_createSNPgenome.out, SNPsplit_createSNPgenome.err
jobid: 8
resources: tmpdir=/projects/allelespecificchromatinmouse/work/MouseSeqData/temp
Both files, SNPsplit_createSNPgenome.out
& SNPsplit_createSNPgenome.err
, are empty.
The directory snp_genome/CAST_EiJ_C57BL_6NJ_dual_hybrid.based_on_GRCm38_105_Mapping_N-masked
contains N-masked fasta files for all chromosomes.
Thanks again :)
Best, Julian
Hi everyone,
i am trying to analyse ATAC-seq data with snakepipes. Currently, I am facing an error during the DNA-mapping workflow. Before that, I have created an index for GRCm38. I have crossed samples from CAST_EiJ and C57BL_6NJ. Thus, I use the allelic-mapping mode and pass a SNP file to the pipeline:
DNA-mapping -i /projects/allelespecificchromatinmouse/work/ATAC/X204SC21092819-Z01-F001_01/raw_data/F2022YB/ -o /projects/allelespecificchromatinmouse/work/MouseSeqData/results/DNA-Mapping/F2022YB/ --local --mode allelic-mapping --VCFfile /projects/allelespecificchromatinmouse/work/MouseSeqData/help_data/mgp.v5.merged.snps_all.dbSNP142.vcf --strains 'CAST_EiJ,C57BL_6NJ' --ext .fq.gz --reads '_1' '_2' GRCm38_105_Mapping
I get the following Error-message:
bowtie2.index.err:
bowtie2.index.out is empty.
Do you have any idea how to fix this? If you need more information just let me know.
Thanks a lot for your help :)
(I have seen issue #517 regarding the same problem. Unfortunately that did not help.)
Best Julian