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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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test make failed #343

Closed virenar closed 6 years ago

virenar commented 6 years ago

I got following error message when I was trying to test the installation -

Traceback (most recent call last):
  File "../cnvkit.py", line 13, in <module>
    args.func(args)
  File "/Users/vamin/projects/CNV/cnvkit/cnvlib/commands.py", line 1709, in _cmd_export_nbo
    args.min_variant_depth, args.zygosity_freq)
  File "/Users/vamin/projects/CNV/cnvkit/cnvlib/cmdutil.py", line 25, in load_het_snps
    skip_somatic=True)
  File "/Users/vamin/projects/CNV/cnvkit/skgenome/tabio/__init__.py", line 76, in read
    dframe = reader(infile, **kwargs)
  File "/Users/vamin/projects/CNV/cnvkit/skgenome/tabio/vcfio.py", line 27, in read_vcf
    % exc)
ValueError: Must give a VCF filename, not open file handle: 'module' object has no attribute 'VariantFile'
make: *** [p2-9_2.nexus-ogt] Error 1
make: *** Waiting for unfinished jobs....

I have installed in macos (v10.13.4) from source. I installed all the dependencies R and Python. Here is the full output-

mac01:test vamin$ make -j
python ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt
python ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns
python ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns
python ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns
python ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns
python ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns
python ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns
python ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns
python ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input
python ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \
        --mean --median --mode \
        --stdev --mad --mse --iqr --bivar \
        --ci --pi --sem
python ../cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \
        --ci -b 50 -a 0.5
python ../cnvkit.py metrics  build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv
python ../cnvkit.py metrics  build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv
python ../cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv
Treating sample p2-9_2 as male
Rescaling sample with purity 0.65, ploidy 2
Wrote build/p2-9_2.call.cns with 57 regions
Treating sample p2-20_4 as male
Rescaling sample with purity 0.65, ploidy 2
Treating sample p2-5_5 as male
Rescaling sample with purity 0.65, ploidy 2
Wrote build/p2-20_4.call.cns with 65 regions
Treating sample p2-20_1 as male
Rescaling sample with purity 0.65, ploidy 2
Wrote build/p2-5_5.call.cns with 49 regions
Wrote build/p2-20_1.call.cns with 78 regions
Treating sample p2-20_3 as male
Rescaling sample with purity 0.65, ploidy 2
Treating sample p2-20_5 as male
Rescaling sample with purity 0.65, ploidy 2
Treating sample p2-20_2 as male
Rescaling sample with purity 0.65, ploidy 2
Wrote build/p2-20_3.call.cns with 48 regions
Wrote build/p2-20_5.call.cns with 64 regions
Wrote build/p2-20_2.call.cns with 77 regions
python ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf
python ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed
Traceback (most recent call last):
  File "../cnvkit.py", line 13, in <module>
    args.func(args)
  File "/Users/vamin/projects/CNV/cnvkit/cnvlib/commands.py", line 1709, in _cmd_export_nbo
    args.min_variant_depth, args.zygosity_freq)
  File "/Users/vamin/projects/CNV/cnvkit/cnvlib/cmdutil.py", line 25, in load_het_snps
    skip_somatic=True)
  File "/Users/vamin/projects/CNV/cnvkit/skgenome/tabio/__init__.py", line 76, in read
    dframe = reader(infile, **kwargs)
  File "/Users/vamin/projects/CNV/cnvkit/skgenome/tabio/vcfio.py", line 27, in read_vcf
    % exc)
ValueError: Must give a VCF filename, not open file handle: 'module' object has no attribute 'VariantFile'
make: *** [p2-9_2.nexus-ogt] Error 1
make: *** Waiting for unfinished jobs....
Wrote p2-9_2-metrics.tsv
Wrote p2-5_5-metrics.tsv
Wrote p2-9_2.theta2.input
Treating sample p2-5_5.call as male
Treating sample p2-9_2.call as male
Treating sample p2-20_1.call as male
Treating sample p2-20_2.call as male
Treating sample p2-9_2.call as male
Treating sample p2-20_3.call as male
Treating sample p2-20_4.call as male
Treating sample p2-20_5.call as male
Wrote p2-all.bed
Wrote p2-20-metrics.tsv
Wrote p2-9_2.vcf
Wrote p2-5_5-segmetrics.cns with 49 regions
Wrote p2-9_2-segmetrics.cns with 57 regions
mac01:test vamin$
etal commented 6 years ago

Thanks for letting me know, I'll take a look.

etal commented 6 years ago

Which version of pysam are you using? I've tested CNVkit with pysam v0.10.0 through v0.13.0.

virenar commented 6 years ago

I am using v0.14.1. I will try switching to v0.13.0 and will let you know.

etal commented 6 years ago

The TravisCI automated testing system is back up again and looks OK, so I'll assume the test suite is working OK now with the supported versions of pysam. (Please let me know if it's not.)

ttamho commented 6 years ago

I also got the following error when running test: Traceback (most recent call last): File "../cnvkit.py", line 13, in <module> args.func(args) File "/Users/teehee/workspace/cnvkit/cnvlib/commands.py", line 1282, in _cmd_segmetrics args.alpha, args.bootstrap) File "/Users/teehee/workspace/cnvkit/cnvlib/segmetrics.py", line 50, in do_segmetrics np.float_, len(segarr)) ValueError: iterator too short make: *** [p2-9_2-segmetrics.cns] Error 1

Here is the full log: python ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ Created directory build/ Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions python ../cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn Number of target and antitarget files: 3, 3 No FASTA reference genome provided; skipping GC, RM calculations Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=67.2 x 0.532 = 35.7) --> assuming male Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=38.7 x 0.532 = 20.6) --> assuming male Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=94.8 x 0.532 = 50.4) --> assuming male Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=6.53 x 0.809 = 5.28) --> assuming male Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=9.76 x 0.895 = 8.74) --> assuming male Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=18.1 x 0.895 = 16.2) --> assuming male Loading build/p2-20_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-5_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Loading target build/p2-9_5.targetcoverage.cnn Correcting for GC bias... Correcting for density bias... Calculating average bin coverages Calculating bin spreads Loading build/p2-20_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-5_5.antitargetcoverage.cnn Correcting for GC bias... Loading target build/p2-9_5.antitargetcoverage.cnn Correcting for GC bias... Calculating average bin coverages Calculating bin spreads Targets: 89 (1.3392%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) NOTCH2 chr1:120572470-120572622 log2=-2.599 spread=1.522 GAK chr4:896278-896357 log2=-1.523 spread=1.267 MAP3K1 chr5:56111354-56111894 log2=-1.492 spread=1.060 FLT4 chr5:180076418-180076603 log2=-2.232 spread=1.421 DOM3Z chr6:31938905-31939081 log2=-20.033 spread=0.045 " chr6:31939599-31940313 log2=-19.608 spread=0.181 STK19 chr6:31940351-31940562 log2=-19.003 spread=0.189 " chr6:31946632-31946824 log2=-20.060 spread=0.088 " chr6:31947142-31947366 log2=-20.128 spread=0.065 " chr6:31948176-31948360 log2=-19.992 spread=0.148 " chr6:31948382-31948612 log2=-19.780 spread=0.162 " chr6:31948730-31949253 log2=-20.063 spread=0.020 NOTCH4 chr6:32163159-32163956 log2=-19.331 spread=0.202 " chr6:32164046-32164227 log2=-19.777 spread=0.180 " chr6:32164652-32164888 log2=-19.995 spread=0.151 " chr6:32165021-32165403 log2=-19.643 spread=0.195 " chr6:32166163-32166545 log2=-20.057 spread=0.076 " chr6:32166648-32166962 log2=-3.526 spread=5.774 " chr6:32168554-32168821 log2=-19.621 spread=0.193 " chr6:32168844-32169306 log2=-19.700 spread=0.164 " chr6:32169801-32170391 log2=-19.433 spread=0.206 " chr6:32171492-32171691 log2=-20.108 spread=0.103 " chr6:32171861-32172198 log2=-3.146 spread=7.284 " chr6:32178478-32178749 log2=-19.934 spread=0.167 " chr6:32180197-32180441 log2=-10.912 spread=9.531 " chr6:32180544-32180722 log2=-19.700 spread=0.182 " chr6:32180857-32181062 log2=-19.591 spread=0.214 " chr6:32181411-32181646 log2=-19.979 spread=0.168 " chr6:32181832-32182066 log2=-19.971 spread=0.174 " chr6:32182948-32183194 log2=-19.947 spread=0.171 " chr6:32184667-32185079 log2=-19.931 spread=0.162 " chr6:32185720-32185919 log2=-19.724 spread=0.192 " chr6:32187317-32187601 log2=-19.783 spread=0.171 " chr6:32187871-32188094 log2=-19.686 spread=0.190 " chr6:32188127-32188451 log2=-19.636 spread=0.165 " chr6:32188481-32188693 log2=-19.906 spread=0.130 " chr6:32188704-32189133 log2=-19.522 spread=0.199 " chr6:32190258-32190616 log2=-19.586 spread=0.207 " chr6:32190724-32190908 log2=-19.562 spread=0.218 " chr6:32191570-32191668 log2=-19.792 spread=0.174 " chr6:32191676-32191753 log2=-19.393 spread=0.201 CGH chr7:52520101-52520286 log2=-1.534 spread=1.178 SMO chr7:128828938-128829041 log2=-2.070 spread=1.324 GPR124 chr8:37654740-37655077 log2=-1.623 spread=1.026 GPSM1 chr9:139222089-139222248 log2=-4.896 spread=2.116 MRC1 chr10:18136438-18136613 log2=-1.967 spread=3.254 RET chr10:43572644-43572830 log2=-1.394 spread=1.097 FLT3 chr13:28674525-28674708 log2=-2.268 spread=1.749 IRS2 chr13:110438332-110438432 log2=-3.655 spread=2.330 CGH chr14:19220933-19221047 log2=-1.234 spread=1.211 MAP3K9 chr14:71275790-71275923 log2=-2.828 spread=1.943 LTK chr15:41803310-41803809 log2=-1.970 spread=1.452 PDPK1 chr16:2588022-2588201 log2=-1.783 spread=1.088 " chr16:2611404-2611585 log2=-5.189 spread=1.939 " chr16:2611721-2611943 log2=-11.822 spread=9.176 " chr16:2615504-2615725 log2=-20.129 spread=0.003 " chr16:2616307-2616486 log2=-20.077 spread=0.072 " chr16:2631267-2631414 log2=-20.027 spread=0.061 " chr16:2631583-2631734 log2=-20.122 spread=0.087 " chr16:2633363-2633616 log2=-20.108 spread=0.092 BOLA2B chr16:29466011-29466278 log2=-19.007 spread=0.177 MAP2K4 chr17:11924151-11924355 log2=-2.111 spread=1.902 GIPC3 chr19:3585549-3585853 log2=-1.530 spread=1.093 INSR chr19:7293751-7294042 log2=-2.032 spread=1.542 NOTCH3 chr19:15311544-15311749 log2=-1.901 spread=1.207 CD79A chr19:42384673-42384848 log2=-1.888 spread=1.229 CRLF2 chrX:1314835-1315039 log2=-20.125 spread=0.029 " chrX:1317372-1317594 log2=-20.136 spread=0.045 " chrX:1321225-1321435 log2=-19.869 spread=0.196 " chrX:1325274-1325530 log2=-20.131 spread=0.012 " chrX:1327651-1327830 log2=-20.012 spread=0.030 " chrX:1331391-1331576 log2=-20.024 spread=0.051 CGH chrY:2654543-2654722 log2=-4.357 spread=4.442 " chrY:3023482-3023672 log2=-4.960 spread=6.784 " chrY:4564417-4564597 log2=-11.686 spread=9.039 " chrY:7540620-7540741 log2=-5.016 spread=6.755 " chrY:9008607-9008759 log2=-12.124 spread=8.796 " chrY:13131970-13132039 log2=-20.071 spread=0.102 " chrY:13199435-13199623 log2=-4.281 spread=6.165 " chrY:15007107-15007258 log2=-6.946 spread=7.403 " chrY:16504318-16504496 log2=-5.090 spread=6.641 " chrY:18022729-18022918 log2=-5.529 spread=6.991 " chrY:19506485-19506650 log2=-11.896 spread=8.895 " chrY:21033918-21034071 log2=-20.101 spread=0.087 " chrY:22554204-22554385 log2=-6.070 spread=7.225 " chrY:24000593-24000773 log2=-4.446 spread=4.603 " chrY:28462977-28463157 log2=-5.435 spread=7.074 " chrY:28463435-28463622 log2=-11.305 spread=9.238 " chrY:28514033-28514208 log2=-12.104 spread=8.739 Antitargets: 111 (0.8835%) bins failed filters Wrote build/reference-picard.cnn with 19209 regions python ../cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr Processing target: p2-5_5 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-5_5 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.09 x more variable than antitargets Wrote build/p2-5_5.cnr with 19009 regions python ../cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions python ../cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions python ../cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr Processing target: p2-9_2 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-9_2 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.34 x more variable than antitargets Wrote build/p2-9_2.cnr with 19009 regions python ../cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions python ../cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions python ../cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr Processing target: p2-20_1 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_1 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.08 x more variable than antitargets Wrote build/p2-20_1.cnr with 19009 regions python ../cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions python ../cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions python ../cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr Processing target: p2-20_2 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_2 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.04 x more variable than antitargets Wrote build/p2-20_2.cnr with 19009 regions python ../cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions python ../cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions python ../cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr Processing target: p2-20_3 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_3 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Antitargets are 1.01 x more variable than targets Wrote build/p2-20_3.cnr with 19009 regions python ../cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions python ../cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions python ../cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr Processing target: p2-20_4 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_4 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.18 x more variable than antitargets Wrote build/p2-20_4.cnr with 19009 regions python ../cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr Processing target: p2-20_5 Keeping 6557 of 6646 bins Correcting for GC bias... Correcting for density bias... Processing antitarget: p2-20_5 Keeping 12452 of 12563 bins Correcting for GC bias... WARNING: Skipping correction for RepeatMasker bias Targets are 1.60 x more variable than antitargets Wrote build/p2-20_5.cnr with 19009 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote build/p2-5_5.cns with 49 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Dropped 1 / 966 bins on chromosome chr6 Dropped 1 / 5 bins on chromosome chrY Wrote build/p2-9_2.cns with 57 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote build/p2-20_1.cns with 78 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote build/p2-20_2.cns with 77 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote build/p2-20_3.cns with 48 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote build/p2-20_4.cns with 65 regions python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns Segmenting with method 'cbs', significance threshold 0.01, in 2 processes /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote build/p2-20_5.cns with 64 regions python ../cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote p2-5_5-scatter.pdf python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote p2-9_2-scatter.pdf python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf Showing 1498 probes and 0 selected genes in region chr1 /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/signal/_savitzky_golay.py:135: RuntimeWarning: internal gelsd driver lwork query error, required iwork dimension not returned. This is likely the result of LAPACK bug 0038, fixed in LAPACK 3.2.2 (released July 21, 2010). Falling back to 'gelss' driver. coeffs, _, _, _ = lstsq(A, y) Wrote p2-9_2-chr1-scatter.pdf python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf Showing 341 probes and 14 selected genes in region chr9:149999-45000000 Wrote p2-9_2-chr9p-scatter.pdf python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf Showing 186 probes and 2 selected genes in region chr9:0-14504268 Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf python ../cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf Detected file format: bed Showing 43 probes and 1 selected genes in region chr9:2000000-4000000 Showing 54 probes and 1 selected genes in region chr9:8000000-12000000 which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf python ../cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf Treating sample p2-5_5 as male Wrote p2-5_5-diagram.pdf python ../cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf Treating sample p2-9_2 as male Wrote p2-9_2-diagram.pdf python ../cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf Treating sample p2-20_1 as male Wrote p2-20_1-diagram.pdf python ../cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf Treating sample p2-20_2 as male Wrote p2-20_2-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf Treating sample p2-5_5 as male Wrote p2-5_5-cbs-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf Treating sample p2-9_2 as male Wrote p2-9_2-cbs-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf Treating sample p2-20_1 as male Wrote p2-20_1-cbs-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf Treating sample p2-20_2 as male Wrote p2-20_2-cbs-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf Treating sample p2-5_5 as male Wrote p2-5_5-both-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf Treating sample p2-9_2 as male Wrote p2-9_2-both-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf Treating sample p2-20_1 as male Wrote p2-20_1-both-diagram.pdf python ../cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf Treating sample p2-20_2 as male Wrote p2-20_2-both-diagram.pdf which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf python ../cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf Treating sample p2-5_5 as male Treating sample p2-9_2 as male Treating sample p2-20_1 as male Treating sample p2-20_2 as male Treating sample p2-20_3 as male Treating sample p2-20_4 as male Treating sample p2-20_5 as male Wrote heatmap-picard.pdf python ../cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt Found 1 gene breakpoints Wrote p2-9_2-breaks.txt python ../cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt Treating sample p2-9_2 as male Found 322 gene-level gains and losses Wrote p2-9_2-genemetrics.txt python ../cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt Wrote gender-picard.txt python ../cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt /Users/teehee/workspace/cnvkit/cnvlib/export.py:70: FutureWarning: from_items is deprecated. Please use DataFrame.from_dict(dict(items), ...) instead. DataFrame.from_dict(OrderedDict(items)) may be used to preserve the key order. ("GWEIGHT", 1), Wrote p2-all.cdt python ../cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt Wrote p2-all-jtv.txt python ../cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg Wrote p2-all.seg python ../cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus Wrote p2-9_2.nexus python ../cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt Selected test sample NA12882 and control sample NA12878 Loaded 3654 records; skipped: 514 somatic, 394 depth Kept 2631 heterozygous of 3654 VCF records Placed 727 variants into 19009 bins Wrote p2-9_2.nexus-ogt python ../cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns Treating sample p2-5_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-5_5.call.cns with 49 regions python ../cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns Treating sample p2-9_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-9_2.call.cns with 57 regions python ../cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns Treating sample p2-20_1 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_1.call.cns with 78 regions python ../cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns Treating sample p2-20_2 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_2.call.cns with 77 regions python ../cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns Treating sample p2-20_3 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_3.call.cns with 48 regions python ../cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns Treating sample p2-20_4 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_4.call.cns with 65 regions python ../cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns Treating sample p2-20_5 as male Rescaling sample with purity 0.65, ploidy 2 Wrote build/p2-20_5.call.cns with 64 regions python ../cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed Treating sample p2-5_5.call as male Treating sample p2-9_2.call as male Treating sample p2-20_1.call as male Treating sample p2-20_2.call as male Treating sample p2-20_3.call as male Treating sample p2-20_4.call as male Treating sample p2-20_5.call as male Wrote p2-all.bed python ../cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf Treating sample p2-9_2.call as male Wrote p2-9_2.vcf python ../cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input Wrote p2-9_2.theta2.input python ../cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ --mean --median --mode \ --stdev --mad --mse --iqr --bivar \ --ci --pi --sem Traceback (most recent call last): File "../cnvkit.py", line 13, in <module> args.func(args) File "/Users/teehee/workspace/cnvkit/cnvlib/commands.py", line 1282, in _cmd_segmetrics args.alpha, args.bootstrap) File "/Users/teehee/workspace/cnvkit/cnvlib/segmetrics.py", line 50, in do_segmetrics np.float_, len(segarr)) ValueError: iterator too short

etal commented 6 years ago

Thanks for reporting the latest error. It looks like this happened in the development version due to a recent commit. I'll fix it.