#WARNING & ERROR MESSAGE while running merging command of 2nd step

[nitha26]

Hi, I am using Freeze8 latest version of TOPMed pipeline in CentOS (centos-release-7-3.1611.el7.centos.x86_64).
I got the following warning and error message while running the TOPMed pipeline

1)While running merging verifyBamID2 results and X/Y depth results into a single index file (../apigenome/bin/cram-vb-xy-index --index index/list.107.local.crams.index --dir out/sm/ --out out/index/list.107.local.crams.vb_xy.index) I get this warning:

"WARNING: Third column is not given from index/list.107.local.crams.index. Assuming out/sm//YO2152001 4QH/YO21520014QH.bcf is BCF_PATH for line 1. Further warnings will be suppressed
Finished writing out/index/list.107.local.crams.vb_xy.index as the index file containing QC metrics"

Could you please explain why this warning occurs and what should I do to fix it?

2)Next, I ran Step2: Hierarchical merge of variant sites.. command

I have got the following error message

Finished forkExecWait(): ../bcftools/bcftools index out/union/81/b81.chr11_40000001_50000000.merged.sites.bcf
ERROR: Could not successfully finish the command '../bcftools/bcftools index out/union/81/b81.chr11_40000001_50000000.merged.sites.bcf', returning exit code 255
Successfully finished the step3 command '../bcftools/bcftools index out/union/81/b81.chr11_40000001_50000000.merged.sites.bcf'

Why this error is occurring? what are the files need modification?

3. For running the pipeline, what is the minimum samples number required?

Tools version:

1. samtools 1.9-66-gc15e884
   Using htslib 1.9-143-gcda2298
   Copyright (C) 2019 Genome Research Ltd.

2.bcftools 1.9-145-g1de0487
Using htslib 1.9-143-gcda2298
Copyright (C) 2018 Genome Research Ltd.

Thanks.

error-msg.txt