tetedange13
commented
1 year ago Hi @HeejunJang ,
Thanks for reporting this, I just submitted a PR (#764) to fix it => In the meantime, I suggest you use latest stable release of CNVkit instead
Sorry for the inconvenience ! Have a nice day, Felix.
my command was
$CNVKIT/cnvkit.py batch $INPUT/$i".bam" --n \ --targets $REF/bed/mybed.bed \ --fasta $REF/hg19/hg19_1-22-X-Y-M.fa \ --output-reference $FINAL/$i".cnn" \ --output-dir $FINAL
$CNVKIT/cnvkit.py segmetrics -s $FINAL/$i".cn"{s,r} --ci
here's error message
Traceback (most recent call last): File "/work/tools/cnvkit/cnvkit.py", line 9, in
args.func(args)
File "/work/tools/cnvkit/cnvlib/commands.py", line 138, in _cmd_batch
pool.submit(batch.batch_run_sample,
File "/work/tools/cnvkit/cnvlib/parallel.py", line 19, in submit
return SerialFuture(func(*args))
File "/work/tools/cnvkit/cnvlib/batch.py", line 180, in batch_run_sample
cnarr = fix.do_fix(raw_tgt, raw_anti, read_cna(ref_fname),
File "/work/tools/cnvkit/cnvlib/fix.py", line 15, in do_fix
cnarr, ref_matched = load_adjust_coverages(target_raw, reference,
File "/work/tools/cnvkit/cnvlib/fix.py", line 72, in load_adjust_coverages
ok_cvg_indices = ~mask_bad_bins(ref_matched)
File "/work/tools/cnvkit/cnvlib/fix.py", line 127, in mask_bad_bins
lower_gc_bound = min(GC_MIN_FRACTION, GC_MAX_FRACTION)
NameError: name 'GC_MIN_FRACTION' is not defined
CNVkit can't make cns file
please help.