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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Error: NO SIGNAL DATA FOUND IN INPUTFILE #39

Open KaraLayton opened 5 years ago

KaraLayton commented 5 years ago

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

kaichop commented 5 years ago

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton notifications@github.com wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuKPYnkD8EuRE-W9ZYlT0YwXcq8SDks5vf4tsgaJpZM4cqron .

KaraLayton commented 5 years ago

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang notifications@github.com wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton notifications@github.com wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread < https://github.com/notifications/unsubscribe-auth/AFptuKPYnkD8EuRE-W9ZYlT0YwXcq8SDks5vf4tsgaJpZM4cqron

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

kaichop commented 5 years ago

try change Chr to real chromosome name rather than a contig with "_" and "." character. Also, you need to show the actual command and the actual message after you type the detect_cnv.pl command, not just a small part of the output.

On Thu, Apr 11, 2019 at 3:36 PM Kara Layton notifications@github.com wrote:

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang notifications@github.com wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton notifications@github.com wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

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KaraLayton commented 5 years ago

Thanks very much, this helped to get the script running. I'll make sure to provide the complete command next time. I'm also wondering if you could advise the best way to generate an .hmm file for my dataset?

On Thu, 11 Apr 2019 at 16:40, Kai Wang notifications@github.com wrote:

try change Chr to real chromosome name rather than a contig with "_" and "." character. Also, you need to show the actual command and the actual message after you type the detect_cnv.pl command, not just a small part of the output.

On Thu, Apr 11, 2019 at 3:36 PM Kara Layton notifications@github.com wrote:

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang notifications@github.com wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton notifications@github.com wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39#issuecomment-482275520, or mute the thread < https://github.com/notifications/unsubscribe-auth/AFptuI8GL-TC_pX3PnK93qLCNUKq198pks5vf467gaJpZM4cqron

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

kaichop commented 5 years ago

You can just use the default hmm.

On Thu, Apr 11, 2019 at 4:22 PM Kara Layton notifications@github.com wrote:

Thanks very much, this helped to get the script running. I'll make sure to provide the complete command next time. I'm also wondering if you could advise the best way to generate an .hmm file for my dataset?

On Thu, 11 Apr 2019 at 16:40, Kai Wang notifications@github.com wrote:

try change Chr to real chromosome name rather than a contig with "_" and "." character. Also, you need to show the actual command and the actual message after you type the detect_cnv.pl command, not just a small part of the output.

On Thu, Apr 11, 2019 at 3:36 PM Kara Layton notifications@github.com wrote:

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang notifications@github.com wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton < notifications@github.com> wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39#issuecomment-482275520, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39#issuecomment-482297036, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuJL1TUKogTTajl8oowbz4LE9VIe6ks5vf5mbgaJpZM4cqron .

KaraLayton commented 5 years ago

Thanks very much for your help. The script is working but it's ignoring chromosomes 23-39. I'm assuming this has something to do with the program being used for human models, whereas I'm using it for salmonids. I'm wondering if you have any advice on how to compensate for this larger number of chromosomes? Thanks in advance, Kara

On Thu, 11 Apr 2019 at 17:48, Kai Wang notifications@github.com wrote:

You can just use the default hmm.

On Thu, Apr 11, 2019 at 4:22 PM Kara Layton notifications@github.com wrote:

Thanks very much, this helped to get the script running. I'll make sure to provide the complete command next time. I'm also wondering if you could advise the best way to generate an .hmm file for my dataset?

On Thu, 11 Apr 2019 at 16:40, Kai Wang notifications@github.com wrote:

try change Chr to real chromosome name rather than a contig with "_" and "." character. Also, you need to show the actual command and the actual message after you type the detect_cnv.pl command, not just a small part of the output.

On Thu, Apr 11, 2019 at 3:36 PM Kara Layton notifications@github.com wrote:

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang notifications@github.com wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton < notifications@github.com> wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39#issuecomment-482275520, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39#issuecomment-482297036, or mute the thread < https://github.com/notifications/unsubscribe-auth/AFptuJL1TUKogTTajl8oowbz4LE9VIe6ks5vf5mbgaJpZM4cqron

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

kaichop commented 5 years ago

add -lastchr 29 to the command line.

On Tue, Apr 16, 2019 at 3:10 PM Kara Layton notifications@github.com wrote:

Thanks very much for your help. The script is working but it's ignoring chromosomes 23-39. I'm assuming this has something to do with the program being used for human models, whereas I'm using it for salmonids. I'm wondering if you have any advice on how to compensate for this larger number of chromosomes? Thanks in advance, Kara

On Thu, 11 Apr 2019 at 17:48, Kai Wang notifications@github.com wrote:

You can just use the default hmm.

On Thu, Apr 11, 2019 at 4:22 PM Kara Layton notifications@github.com wrote:

Thanks very much, this helped to get the script running. I'll make sure to provide the complete command next time. I'm also wondering if you could advise the best way to generate an .hmm file for my dataset?

On Thu, 11 Apr 2019 at 16:40, Kai Wang notifications@github.com wrote:

try change Chr to real chromosome name rather than a contig with "_" and "." character. Also, you need to show the actual command and the actual message after you type the detect_cnv.pl command, not just a small part of the output.

On Thu, Apr 11, 2019 at 3:36 PM Kara Layton < notifications@github.com> wrote:

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang notifications@github.com wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton < notifications@github.com> wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/39, or mute the thread <

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

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-- Kara Layton, PhD Postdoctoral Fellow Ocean Frontier Institute Department of Ocean Sciences Memorial University of Newfoundland klayton@mun.ca

Bedford Institute of Oceanography 1 Challenger Drive Dartmouth, NS B2Y 4A2

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KaraLayton commented 5 years ago

Thanks very much, it was successful! Cheers, Kara

On Tue, 16 Apr 2019 at 17:08, Kai Wang notifications@github.com wrote:

add -lastchr 29 to the command line.

On Tue, Apr 16, 2019 at 3:10 PM Kara Layton notifications@github.com wrote:

Thanks very much for your help. The script is working but it's ignoring chromosomes 23-39. I'm assuming this has something to do with the program being used for human models, whereas I'm using it for salmonids. I'm wondering if you have any advice on how to compensate for this larger number of chromosomes? Thanks in advance, Kara

On Thu, 11 Apr 2019 at 17:48, Kai Wang notifications@github.com wrote:

You can just use the default hmm.

On Thu, Apr 11, 2019 at 4:22 PM Kara Layton notifications@github.com wrote:

Thanks very much, this helped to get the script running. I'll make sure to provide the complete command next time. I'm also wondering if you could advise the best way to generate an .hmm file for my dataset?

On Thu, 11 Apr 2019 at 16:40, Kai Wang notifications@github.com wrote:

try change Chr to real chromosome name rather than a contig with "_" and "." character. Also, you need to show the actual command and the actual message after you type the detect_cnv.pl command, not just a small part of the output.

On Thu, Apr 11, 2019 at 3:36 PM Kara Layton < notifications@github.com> wrote:

Thanks so much for your response. This what I see at the head of my pfb and signal files:

Name Chr Position H12_IB58_Axiom_Char_P045_GDL0632957.CEL.Log R Ratio H12_IB58_Axiom_Char_P045_GDL0632957.CEL.B Allele Freq AX-105314453 NC_036870.1 9909747 -0.0975 0.9980

Name Chr Position PFB AX-105314453 NC_036870.1 9909747 0.839

It looks like the markers are properly annotated in both, but I'm not sure if I'm misinterpreting.

Thanks again, Kara

On Thu, 11 Apr 2019 at 16:23, Kai Wang <notifications@github.com

wrote:

It means these markers are not annotated in your PFB file. You can just "head" these files to see what's the problem.

On Thu, Apr 11, 2019 at 3:22 PM Kara Layton < notifications@github.com> wrote:

Hi there, I'm trying to execute the detect_cnv.pl script and I keep coming across the same error. It reads: NOTICE: Reading LRR and BAF values for from gw6.H11_IB58_Axiom_Char_P040_1051729031 ... Done with 0 records in 0 chromosomes (13664 records are discarded due to lack of PFB information for the markers) ERROR: NO SIGNAL DATA FOUND IN INPUTFILE gw6.H11_IB58_Axiom_Char_P040_1051729031 WARNING: Skipping gw6.H11_IB58_Axiom_Char_P040_1051729031 since no signal values can be retrieved from the file My pfb and signal files have values for pfb, log r ratio, and b allele freq, but the files aren't being read properly. I'm wondering if you've come across this issue before? Thank you in advance!

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rashindrie commented 3 years ago

Hi,

I am running into the same problem when I run the following command:

PennCNV-1.0.5/detect_cnv.pl -test -hmm PennCNV-1.0.5/lib/hh550.hmm -pfb out_file.pfb 06-017.txt -log sample_06-017_.log -out 06-017.rawcnv

Log file is attached: sample06-017.log

`$ head out_file.pfb Name Chr Position PFB 1:103380393 1:103380393 1:103380393 0.954 1:109439680 1:109439680 1:109439680 0.001 1:110198788 1:110198788 1:110198788 0.004 1:110201112 1:110201112 1:110201112 0.004 1:110201667 1:110201667 1:110201667 0.991 1:110202904 1:110202904 1:110202904 0.002 1:110203240 1:110203240 1:110203240 0.986 1:110203911 1:110203911 1:110203911 0.99 1:110206675 1:110206675 1:110206675 0.008

$ head 06-017.txt Name 06-017.Log R Ratio 06-017.B Allele Freq 1:103380393 0.4025 1.0000 1:109439680 0.3376 0.0000 1:110198788 0.1123 0.0000 1:110201112 -0.2381 0.0026 1:110201667 -0.1368 1.0000 1:110202904 -0.0543 0.0041 1:110203240 0.0853 1.0000 1:110203911 -0.1588 1.0000 1:110206675 0.0026 0.0000`

try change Chr to real chromosome name rather than a contig with "_" and "." character.

What does this mean? Could you give an example please. This is my first time working with SNP data so I am unfamiliar of the terms.

Thanks

kaichop commented 3 years ago

In the PFB file, the Name, Chr and Position are identical, and Chr should be chromosome (1), position should be position (103380393) Ideally put a less confusing identifier to the Name such as rs number or other types of identifiers, without any strange characters.

On Sun, Jun 20, 2021 at 6:31 AM Rashindrie @.***> wrote:

Hi,

I am running into the same problem when I run the following command:

PennCNV-1.0.5/detect_cnv.pl -test -hmm PennCNV-1.0.5/lib/hh550.hmm -pfb out_ILGSA24-17204.pfb ILGSA24-17204_processed2/06-017.txt -log sample06-017.log -out ILGSA24-17204_processed2/06-017.rawcnv

Log file is attached: sample06-017.log https://github.com/WGLab/PennCNV/files/6682110/sample_06-017_.log

`$ head out_ILGSA24-17204.pfb Name Chr Position PFB 1:103380393 1:103380393 1:103380393 0.954 1:109439680 1:109439680 1:109439680 0.001 1:110198788 1:110198788 1:110198788 0.004 1:110201112 1:110201112 1:110201112 0.004 1:110201667 1:110201667 1:110201667 0.991 1:110202904 1:110202904 1:110202904 0.002 1:110203240 1:110203240 1:110203240 0.986 1:110203911 1:110203911 1:110203911 0.99 1:110206675 1:110206675 1:110206675 0.008

$ head ILGSA24-17204_processed2/06-017.txt Name 06-017.Log R Ratio 06-017.B Allele Freq 1:103380393 0.4025 1.0000 1:109439680 0.3376 0.0000 1:110198788 0.1123 0.0000 1:110201112 -0.2381 0.0026 1:110201667 -0.1368 1.0000 1:110202904 -0.0543 0.0041 1:110203240 0.0853 1.0000 1:110203911 -0.1588 1.0000 1:110206675 0.0026 0.0000`

try change Chr to real chromosome name rather than a contig with "_" and "." character.

What does this mean? Could you give an example please. This is my first time working with SNP data so I am unfamiliar of the terms.

Thanks

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rashindrie commented 3 years ago

Hi @kaichop,

I see. So I have not generated the PFB file correctly.

This is an extract from one of the Illumina input files I was provided with for the analysis. The above intensity file (06-017.txt) was generated using one of such inputs.

Screen Shot 2021-06-22 at 9 19 58 am

I can see that the Sample Name column is empty. This must be the cause of the issue I guess.

I am assuming the Sample Name column should be populated during the process of creating these Illumina files itself. Correct me if I'm wrong.

Or is there a way for me to do it as well?

Thanks, Rashindrie

rashindrie commented 3 years ago

Hi,

I was able to generate the PFB after fixing several issues.

  1. Problem 1: I was not providing the -listfile argument correctly for the PFB generation. Fix 1: Created a new text file "intensity_files.txt" and added absolute paths to all the intensity files. For example, the contents of this file should like below:
 /my_absolute_path/sample_01.txt
 /my_absolute_path/sample_02.txt
 /my_absolute_path/sample_03.txt
...... and so on...

Then, used the following command for PFB generation

PennCNV-1.0.5/compile_pfb.pl -listfile /my_absolute_path/intensity_files.txt -output data/PFB_ILGDH.pfb
  1. Problem 2: The default script to generate intensity files was only extracting name, LRR and BAF information but not Chr and Position info Fix 2: Modified split_illumina_report.pl to also extract Chr, and Position columns when creating the intensity files.

And that was it. I was successfully able to generate BAF files after that (with some warnings ofc - not a perfect world xD) !