Dear All, I have a large set of bovine samples (~2700 bam files, on average about 10x coverage) that I want to run mpileup on. I am getting an error that seems to indicate that there is a hard coded limit of bam files in Samtools.
I am running Samtools 1.3 using the following command: module load samtools/1.3.1 module load bcftools/1.3.1 samtools mpileup -r Chr2:10000-20000 -ugf reference.fa -b bams.txt -t AD,INFO/AD,ADF,ADR,SP | bcftools call -mv -> 1000Sam1.3.test.vcf I get this error: [mpileup] fail to load index for XXX.bam Failed to open -: unknown file type I have gone and regenerated the XXX.bam.bai file (with Samtools1.3.1), and rerun and I still get the same error. I have then removed the first bam file in "bams.txt" and then the error moves to the next bam file in the list after XXX.bam, lets call it YYY.bam. [mpileup] fail to load index for YYY.bam Failed to open -: unknown file type This seems to indicate that XXX.bam.bai is OK, but that I hit another cryptic error in Samtools. Possibly a limit of number of bams? XXX.bam is the 1995th file, and YYY.bam is the 1996th. When YYY.bam becomes the 1995th (because I removed an earlier bam file in the list) file the error passes XXX.bam and prints at YYY.bam. Any help would be greatly appreciated. Cheers, Hans PS: there is a post on limit number of bams on the list already from 2012, it is related to the file name size, I have checked that that is not an issue in my case. ----------------------------------------- Dr. Hans Daetwyler | Research Leader Computational Biology Biosciences Research | Agriculture Victoria | DEDJTR Senior Research Fellow | Applied Systems Biology | La Trobe University AgriBio Centre, 5 Ring Rd., Bundoora 3083, Victoria T: 03 9032 7037 | E: hans.daetwy...@ecodev.vic.gov.au ******************************************************************************** Department of Economic Development, Jobs, Transport and Resources, Government of Victoria, Victoria, Australia. This email, and any attachments, may contain privileged and confidential information. If you are not the intended recipient, you may not distribute or reproduce this e-mail or the attachments. If you have received this message in error, please notify us by return email. ********************************************************************************
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