Open mabba777 opened 1 year ago
So the crucial error line is this:
A USER ERROR has occurred: Couldn't read file file:///var/pipeline/ref/GRCm38.p6/MGP.v5.snp_and_indels.exclude_wild.vcf.gz. Error was: It doesn't exist.
Apparently the script "Preparation_GenerateSangerMouseDB.sh" was not successfully executed and the SANGER mouse SNP-DB is missing. This (one-time) processing involves some heavy downloads, so maybe this failed for you in the initial genome generation? The final file should be ~3GB, constructed from the individual SANGER VCF files. In theory you can just execute that script either within or outside of docker to generate the missing files.
You are right, the MGP.v5.snp_and_indels.exclude_wild.vcf.gz was not generated. I have tried executing the Preparation_GenerateSangerMouseDB.sh (provided with the Docker and the updated version) without success. I think the issue is that there is a missing url when trying: wget -nv -c -r -P ftp://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-1505-SNPs_Indels/strain_specific_vcfs/ Where can I download the MGP.v5.snp_and_indels.exclude_wild.vcf.gz file?
Dear, I was running MoCaSeq test, the reference genome was properly downloaded and indexed and the fastq files were aligned and processed in the /temp folder, but didn't appear in the MoCaSeq_test/results/BAM folder, and for that no variants are detected. MoCaSeq_Test.Normal.cleaned.sorted.readgroups.marked.bam MoCaSeq_Test.Normal.cleaned.sorted.readgroups.marked.bam.bai MoCaSeq_Test.Tumor.cleaned.sorted.readgroups.marked.bam MoCaSeq_Test.Tumor.cleaned.sorted.readgroups.marked.bam.bai Please find attached the MoCaSeq report MoCaSeq_Test.report.txt
Also, I was running a normal-tumor real case reproducing the same issue but also with some problem to mark read duplicates during BAM processing, see report:
C7HI1.report.txt
Do you have any advice? Thanks a lot.