bam2seqz generates seqz files with missing chromosomes

[William Waddingham]

Hi,

Apologies if topic already covered, grateful for any suggestions.  I am analysing WES data aligned against Hg19.  Bam2seqz runs fine but the seqz.gz files generated only containg ChrM (no other chromosomes).  I have tried with older versions of samtools same result.  Wondered if Chr annotations were different in my Bams to the hg19.fa but they seem to match (albeit order is different).  Below an example script and an error message generated when running with samtools 1.2.

Many thanks,

Will

~/.local/bin/sequenza-utils bam2seqz -n ~/progressorGastricProject/data/1.3.bamFiles/13-4/M2-13-4B6MC.mkdub.bam -t ~/progressorGastricProject/data/1.3.bamFiles/13-4/J2-13-4B2patch1IM.mkdub.bam --fasta ~/progressorGastricProject/data/referenceFiles/hg19.fa \

(run on Python 2.7 and samtools 1.9)
-gc ~/progressorGastricProject/data/referenceFiles/hg19.gc50Base.wig.gz -o ~/progressorGastricProject/data/1.5.sequenza/13-4/J2-13-4B2patch1IM.seqz.gz

[William Waddingham]

Sorry error message attached now