Hi, I was trying to call CNV in yeast genomes by running
cnvkit.py batch Sample1.bam Sample2.bam -n Control1.bam Control2.bam -m wgs -f sacCer.fasta --annotate refFlat.txt
command, but I ran into the error below:
Traceback (most recent call last): File "/Users/wwei/anaconda2/bin/cnvkit.py", line 13, in <module> args.func(args) File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/commands.py", line 113, in _cmd_batch args.count_reads, args.method) File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/batch.py", line 74, in batch_make_reference bam_fname, *autobin_args, bp_per_bin=50000.) File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/autobin.py", line 96, in do_autobin tgt_bin_size = depth2binsize(tgt_depth, target_min_size, target_max_size) File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/autobin.py", line 62, in depth2binsize bin_size = int(round(bp_per_bin / depth)) ValueError: cannot convert float NaN to integer
When I omit the
--annotate option, it worked fine and I was able to obtain the
.cns files. Just wondering if anyone has ever encountered similar issues and if there's anything I could do about it. Thank you.