Error in bam2h5.py

[danliangunc]

Hi,

I have two problems when I am using bam2h5.py. Here is my command line python3 /nas/longleaf/apps/wasp/2018-07/WASP/CHT/bam2h5.py --chrom hg38.chromInfo.txt.gz --snp_index $DIR/snp_index.h5 --snp_tab $DIR/snp_tab.h5 --haplotype $DIR/haplotypes.h5 --samples Samples.txt --individual D10_DNAID194 --ref_as_counts ref_as_counts.R00AL101.h5 --alt_as_counts alt_as_counts.R00AL101.h5 --other_as_counts other_as_counts.R00AL101.h5 --read_counts read_counts.R00AL101.h5 R00AL101.keep.uniq.NoMTBlist.bam

1) When I used --sample and --individual, I got the error Traceback (most recent call last): File "/nas/longleaf/apps/wasp/2018-07/WASP/CHT/bam2h5.py", line 755, in <module> main() File "/nas/longleaf/apps/wasp/2018-07/WASP/CHT/bam2h5.py", line 615, in main ind_idx = lookup_individual_index(args.samples, args.individual) File "/nas/longleaf/apps/wasp/2018-07/WASP/CHT/bam2h5.py", line 594, in lookup_individual_index (ind_name, population, samples_file)) ValueError: individual D10_DNAID194 (with population=None) is not in samples file /proj/steinlab/projects/R00/atac-qtl/WASPResult/RemappedFiles/Samples.txt

But I do checked the Samples.txt, it contains the IID D10_DNAID194. I am confused about why the code can not recognize the IID.

2) Then I tried not using --haplotype (also removed --sample and --individual), here came another error Traceback (most recent call last): File "/nas/longleaf/apps/wasp/2018-07/WASP/CHT/bam2h5.py", line 755, in <module> main() File "/nas/longleaf/apps/wasp/2018-07/WASP/CHT/bam2h5.py", line 650, in main if args.text_counts is not None: AttributeError: 'Namespace' object has no attribute 'text_counts'

I do not have ideas about both of the errors, do you have any suggestion?

Thanks!

Dan