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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Error: cannot read from HMM file #31

Closed argossy closed 5 years ago

argossy commented 6 years ago

Hi I tried to run PennCNV with the following command line and error message below. The message says cannot find hmm file but I am pretty sure HMM is in my current folder. my version of software is: PennCNV 1.04 Perl 5.8.7 Thank you

command line: detect_cnv.pl -test -hmm affygw6.hmm -pfb affy_LAT_cnv_v0.pfb --chrx --gcmodelfile file.gcmodel -conf -log affy_lat_cnv_chrX.log -out affy_lat_rawcnv_chrX.txt --listfile cnv_filelist.txt

the output error is shown below: NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file affy_lat_cnv_chrX.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from affy_LAT_cnv_v0.pfb ... Done with 816889 records (115 records in chr MT were discarded) NOTICE: Reading LRR and BAF values for from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt ... Done with 816889 records in 24 chromosomes (115 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from -0.0513 to -0.0291, GCWF changes from -0.0459 to -0.0165 NOTICE: Data from chromosome 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,Y will not be used in analysis NOTICE: quality summary for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt: LRR_Xmean=0.0174 LRR_Xmedian=0.0325 LRR_XSD=0.4295 BAF_Xhet=0.2941 NOTICE: Sample sex for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt is predicted as 'female' based on BAF heterozygosity rate (this is different from genotype heterozygosity rate!) for chrX (0.294122300450914) WARNING: Sample from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt does not pass quality control criteria due to its large SD for LRR (0.429494920336252)! WARNING: Small-sized CNV calls may not be reliable and should be interpreted with caution! kc.pm module run-time error (use eval{} in Perl to catch the error) ... Error: cannot read from HMM file at detect_cnv.pl line 850.

kaichop commented 6 years ago

are you sure affygw6.hmm file is at the current directly and it is readable by you?

On Fri, Oct 5, 2018 at 11:54 AM argossy notifications@github.com wrote:

Hi I tried to run PennCNV with the following command line and error message below. The message says cannot find hmm file but I am pretty sure HMM is in my current folder. my version of software is: PennCNV 1.04 Perl 5.8.7 Thank you

command line: detect_cnv.pl -test -hmm affygw6.hmm -pfb affy_LAT_cnv_v0.pfb --chrx --gcmodelfile file.gcmodel -conf -log affy_lat_cnv_chrX.log -out affy_lat_rawcnv_chrX.txt --listfile cnv_filelist.txt

the output error is shown below: NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file affy_lat_cnv_chrX.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from affy_LAT_cnv_v0.pfb ... Done with 816889 records (115 records in chr MT were discarded) NOTICE: Reading LRR and BAF values for from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt ... Done with 816889 records in 24 chromosomes (115 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from -0.0513 to -0.0291, GCWF changes from -0.0459 to -0.0165 NOTICE: Data from chromosome 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,Y will not be used in analysis NOTICE: quality summary for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt: LRR_Xmean=0.0174 LRR_Xmedian=0.0325 LRR_XSD=0.4295 BAF_Xhet=0.2941 NOTICE: Sample sex for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt is predicted as 'female' based on BAF heterozygosity rate (this is different from genotype heterozygosity rate!) for chrX (0.294122300450914) WARNING: Sample from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt does not pass quality control criteria due to its large SD for LRR (0.429494920336252)! WARNING: Small-sized CNV calls may not be reliable and should be interpreted with caution! kc.pm module run-time error (use eval{} in Perl to catch the error) ... Error: cannot read from HMM file at detect_cnv.pl line 850.

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argossy commented 6 years ago

pretty sure. see the command line below:

[kxia@b1003 penncnv]$ less ./affygw6.hmm M=6 N=6 A: 0.970398187 0.001735703 0.027178018 0.000000001 0.000063124 0.000624972 0.000219825 0.975495935 0.023509309 0.000000001 0.000774933 0.000000001 0.000005561 0.000021295 0.999964307 0.000000001 0.000005887 0.000002955 0.000049998 0.000049998 0.000049998 0.999750015 0.000049998 0.000049998 0.000000001 0.000222369 0.018829149 0.000000001 0.980948481 0.000000003 0.000000001 0.000029707 0.038600420 0.000000001 0.000000176 0.961369700 B: 0.950000 0.000001 0.050000 0.000001 0.000001 0.000001 0.000001 0.950000 0.050000 0.000001 0.000001 0.000001 0.000001 0.000001 0.999995 0.000001 0.000001 0.000001 0.000001 0.000001 0.050000 0.950000 0.000001 0.000001 0.000001 0.000001 0.050000 0.000001 0.950000 0.000001 0.000001 0.000001 0.050000 0.000001 0.000001 0.950000 pi: 0.000001 0.000500 0.999000 0.000001 0.000500 0.000001 B1_mean: -1.704554 -0.526063 0.000000 100.000000 0.342932 0.597818 B1_sd: 0.721051 0.234825 0.231839 0.231839 0.254571 0.229630 B1_uf: 0.030000 B2_mean: 0.000000 0.250000 0.333333 0.500000 0.500000 B2_sd: 0.072306 0.050571 0.060498 0.072166 0.226925 B2_uf: 0.030000 B3_mean: -1.716570 -0.527903 0.000000 0.000000 0.343703 0.599012 B3_sd: 0.904104 0.313739 0.307288 0.307288 0.273765 0.299274 B3_uf: 0.030000 [kxia@b1003 penncnv]$ /nas/longleaf/home/kxia/software/PennCNV-1.0.4/detect_cnv.pl -test -hmm ./affygw6.hmm -pfb affy_LAT_cnv_v0.pfb --chrx --gcmodelfile file.gcmodel -conf -log affy_lat_cnv_chrX.log -out affy_lat_rawcnv_chrX.txt --listfile cnv_filelist.txt NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file affy_lat_cnv_chrX.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from affy_LAT_cnv_v0.pfb ... Done with 816889 records (115 records in chr MT were discarded) NOTICE: Reading LRR and BAF values for from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt ... Done with 816889 records in 24 chromosomes (115 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from -0.0513 to -0.0291, GCWF changes from -0.0459 to -0.0165 NOTICE: Data from chromosome 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,Y will not be used in analysis NOTICE: quality summary for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt: LRR_Xmean=0.0174 LRR_Xmedian=0.0325 LRR_XSD=0.4295 BAF_Xhet=0.2941 NOTICE: Sample sex for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt is predicted as 'female' based on BAF heterozygosity rate (this is different from genotype heterozygosity rate!) for chrX (0.294122300450914) WARNING: Sample from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt does not pass quality control criteria due to its large SD for LRR (0.429494920336252)! WARNING: Small-sized CNV calls may not be reliable and should be interpreted with caution! kc.pm module run-time error (use eval{} in Perl to catch the error) ... Error: cannot read from HMM file at /nas/longleaf/home/kxia/software/PennCNV-1.0.4/detect_cnv.pl line 850.

kaichop commented 6 years ago

try use affygw6.hmm, not "./affygw6.hmm" in the command line.

On Fri, Oct 5, 2018 at 12:02 PM argossy notifications@github.com wrote:

pretty sure. see the command line below:

[kxia@b1003 penncnv]$ less ./affygw6.hmm M=6 N=6 A: 0.970398187 0.001735703 0.027178018 0.000000001 0.000063124 0.000624972 0.000219825 0.975495935 0.023509309 0.000000001 0.000774933 0.000000001 0.000005561 0.000021295 0.999964307 0.000000001 0.000005887 0.000002955 0.000049998 0.000049998 0.000049998 0.999750015 0.000049998 0.000049998 0.000000001 0.000222369 0.018829149 0.000000001 0.980948481 0.000000003 0.000000001 0.000029707 0.038600420 0.000000001 0.000000176 0.961369700 B: 0.950000 0.000001 0.050000 0.000001 0.000001 0.000001 0.000001 0.950000 0.050000 0.000001 0.000001 0.000001 0.000001 0.000001 0.999995 0.000001 0.000001 0.000001 0.000001 0.000001 0.050000 0.950000 0.000001 0.000001 0.000001 0.000001 0.050000 0.000001 0.950000 0.000001 0.000001 0.000001 0.050000 0.000001 0.000001 0.950000 pi: 0.000001 0.000500 0.999000 0.000001 0.000500 0.000001 B1_mean: -1.704554 -0.526063 0.000000 100.000000 0.342932 0.597818 B1_sd: 0.721051 0.234825 0.231839 0.231839 0.254571 0.229630 B1_uf: 0.030000 B2_mean: 0.000000 0.250000 0.333333 0.500000 0.500000 B2_sd: 0.072306 0.050571 0.060498 0.072166 0.226925 B2_uf: 0.030000 B3_mean: -1.716570 -0.527903 0.000000 0.000000 0.343703 0.599012 B3_sd: 0.904104 0.313739 0.307288 0.307288 0.273765 0.299274 B3_uf: 0.030000 [kxia@b1003 penncnv]$ /nas/longleaf/home/kxia/software/PennCNV-1.0.4/ detect_cnv.pl -test -hmm ./affygw6.hmm -pfb affy_LAT_cnv_v0.pfb --chrx --gcmodelfile file.gcmodel -conf -log affy_lat_cnv_chrX.log -out affy_lat_rawcnv_chrX.txt --listfile cnv_filelist.txt NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file affy_lat_cnv_chrX.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from affy_LAT_cnv_v0.pfb ... Done with 816889 records (115 records in chr MT were discarded) NOTICE: Reading LRR and BAF values for from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt ... Done with 816889 records in 24 chromosomes (115 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from -0.0513 to -0.0291, GCWF changes from -0.0459 to -0.0165 NOTICE: Data from chromosome 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,Y will not be used in analysis NOTICE: quality summary for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt: LRR_Xmean=0.0174 LRR_Xmedian=0.0325 LRR_XSD=0.4295 BAF_Xhet=0.2941 NOTICE: Sample sex for affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt is predicted as 'female' based on BAF heterozygosity rate (this is different from genotype heterozygosity rate!) for chrX (0.294122300450914) WARNING: Sample from affy_cnv/261_0261-1_V3_D270_8000000628_F09_LAT.cnv.txt does not pass quality control criteria due to its large SD for LRR (0.429494920336252)! WARNING: Small-sized CNV calls may not be reliable and should be interpreted with caution! kc.pm module run-time error (use eval{} in Perl to catch the error) ... Error: cannot read from HMM file at /nas/longleaf/home/kxia/software/PennCNV-1.0.4/detect_cnv.pl line 850.

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argossy commented 6 years ago

I did that before. doesn't change anything

kaichop commented 5 years ago

sorry for losing track of this issue until now. I checked the output again more carefully and see that "WARNING: Small-sized CNV calls may not be reliable and should be interpreted with caution! kc.pm module run-time error (use eval{} in Perl to catch the error) ... Error: cannot read from HMM file at detect_cnv.pl line 850." So there is a possibility that the error is in the kc.pm module itself, and for whatever reason it is reported as HMM file not found after kc.pm run-time error. I would suggest that you recompile the source code (make sure to update to the latest version of PennCNV first).