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Old 05-29-2012, 09:02 PM   #1
jtjli
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Smile CONTRA test files available now

For those of you who have problems running CONTRA for copy number analysis over your exome / targeted resequencing data, I've now made a couple of bam files available on the sourceforge site for testing. (http://contra-cnv.sf.net)

These files have been tested to work. So if CONTRA is somehow not working for you, try these files first to see if the problem lies in your environment or in your bam files.


p.s. sorry about the bad links before for the bam files... they were simply too huge and caused bandwidth problems.
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Old 07-23-2012, 07:06 PM   #2
jtjli
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CONTRA.v2.0.3 is now available on sourceforge. Fixed some bugs, and it is now compatible with the new versions of R.
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Old 01-03-2013, 02:56 PM   #3
id0
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Are the test files expected to yield results?

The three expected table files are produced. Filtered table contains only one result and the VCF file contains no results. Everything seems to be working fine, but I would expect test files to yield more results, so I am not sure if I should be concerned.
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Old 01-31-2013, 02:07 AM   #4
tonio100680
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Default CONTRA help

Hello,

I am a junior bioinformatician! I have to implement CONTRA in laboratory. We work from a target catch (Agilent SureSelect).
For now I installed on a DEBIAN virtual machine CONTRA (python2.6, R 2.11.1 and bedtools). I want to create a control "baseline" from control samples (one bam file per sample and not a bam file per chromosome).

I get this error message:
command:
$ :/ $ python opt/CONTRA.v2.0.3 baseline.py
- target / [PATH] / SureSelect_capture.bed
- files / [PATH] / *. Bam
- output / [PATH] / Baseline /

------- ------ Baseline.py
File: / [PATH] / DZ05.bam
File: / [PATH] / DZ15.bam
File: / [PATH] / DZ25.bam
File: / [PATH] / DZ35.bam
File: / [PATH] / DZ45.bam
Output Directory: / [PATH] / Baseline /
----- ----- Creating output directory
/ [PATH] / Baseline /
/ [PATH] / Baseline / buf
----- ----- Processing Files
/ [PATH] / Baseline/buf/DZ05.bam
/ [PATH] / Baseline/buf/DZ15.bam
/ [PATH] / Baseline/buf/DZ25.bam
/ [PATH] / Baseline/buf/DZ35.bam
/ [PATH] / Baseline/buf/DZ45.bam
chr1
CHR10
/ [PATH] / Baseline/buf/DZ55.bam
Called Effective year throwing terminate instance of 'std :: bad_alloc'
what (): std :: bad_alloc
Traceback (most recent call last):
File "baseline.py", line 149, in <module>
pool.map (processInFile, infiles)
File "/ usr/lib/python2.6/multiprocessing/pool.py", line 148, in map
self.map_async return (func, iterable, chunksize). get ()
File "/ usr/lib/python2.6/multiprocessing/pool.py", line 422, in get
raise self._value
IOError: [Errno 2] No such file or directory: '/ [PATH] / Baseline/buf/DZ15.bam/chr/chr10.txt'

Thank you in advance for your help and excuse me for my english ...

Antoine
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Old 02-11-2013, 03:50 PM   #5
jmatÚs
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Quote:
Originally Posted by jtjli View Post
CONTRA.v2.0.3 is now available on sourceforge. Fixed some bugs, and it is now compatible with the new versions of R.
Quote:
Originally Posted by id0 View Post
Are the test files expected to yield results?

The three expected table files are produced. Filtered table contains only one result and the VCF file contains no results. Everything seems to be working fine, but I would expect test files to yield more results, so I am not sure if I should be concerned.
I'm in the same situation! Any error message, no warnings... but the vcf file stays empty.

Could be possible that the significance filters acts on the adjusted p-value (all of them near 0,99 -all the CNA's don't pass the filter-) and the vcf is allright??

I really want to use it
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Old 02-11-2013, 03:58 PM   #6
jmatÚs
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And when I say that the vcf file is empty, I mean that there is only the header...!
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Old 08-06-2013, 06:46 PM   #7
gary
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I am encountering the same problem as jmatÚs. The vcf file only have headers
I also got some DEBUG massages:

DEBUG 123 genomeCoverageBed -ibam P0667T_GATKrealigned_duplicates_marked.bam -bga -g P0667Test/buf/sample.Genome
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam P0667N_GATKrealigned_duplicates_marked.bam -bga -g P0667Test/buf/sample.Genome

I have tried CONTRA.v2.0.2 and CONTRA.v2.0.4 with both python2.6 and 3.0.
Any suggestions would be appreciated.

Thanks!
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Old 12-11-2013, 12:11 AM   #8
ymc
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What about CoNVex? How come I couldn't find anywhere to download the program?
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Old 12-11-2013, 03:14 PM   #9
jtjli
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ADTEx is the improved version of CoNVEx

http://adtex.sourceforge.net

cheers
jason
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Old 12-11-2013, 05:09 PM   #10
ymc
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Quote:
Originally Posted by jtjli View Post
ADTEx is the improved version of CoNVEx

http://adtex.sourceforge.net

cheers
jason
Thanks a lot for your reply. I will give it a try.
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Old 12-11-2013, 05:36 PM   #11
ymc
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Quote:
Originally Posted by jtjli View Post
ADTEx is the improved version of CoNVEx

http://adtex.sourceforge.net

cheers
jason
Wow. This program is very user friendly compare to Control-FREEC or ExomeCNV.

What about tumor purity estimation? Is it done internally?
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Old 12-12-2013, 04:20 PM   #12
ymc
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Quote:
Originally Posted by jtjli View Post
ADTEx is the improved version of CoNVEx

http://adtex.sourceforge.net

cheers
jason
I noticed that this program generates really huge temp files. For my 4.2G tumor bam and 3.2G normal bam, it generated over 100GB of temp file.

Is it possible to update your program such that I can turn on a flag that gzips the temp files? I think CPU time is cheaper than the I/O time these days. Thanks.

Last edited by ymc; 12-12-2013 at 04:22 PM.
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Old 01-09-2014, 11:45 AM   #13
wolfpack14
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Quote:
Originally Posted by gary View Post
I am encountering the same problem as jmatÚs. The vcf file only have headers
I also got some DEBUG massages:

DEBUG 123 genomeCoverageBed -ibam P0667T_GATKrealigned_duplicates_marked.bam -bga -g P0667Test/buf/sample.Genome
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam P0667N_GATKrealigned_duplicates_marked.bam -bga -g P0667Test/buf/sample.Genome

I have tried CONTRA.v2.0.2 and CONTRA.v2.0.4 with both python2.6 and 3.0.
Any suggestions would be appreciated.

Thanks!
Gary, the DEBUG output is not actually an error. It is a hard coded print function that was added in version 2.0.4. Even if the function runs correctly, it will output that information. Perhaps it was used to diagnose previous bugs, but wasn't commented out by the author...
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Old 01-18-2014, 01:39 AM   #14
ymc
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Can ADTex be used for finding CNVs for normal tissue? If not, what is the best tool for that? Thanks
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Old 07-04-2014, 07:12 AM   #15
mafonso
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Quote:
Originally Posted by id0 View Post
Are the test files expected to yield results?

The three expected table files are produced. Filtered table contains only one result and the VCF file contains no results. Everything seems to be working fine, but I would expect test files to yield more results, so I am not sure if I should be concerned.
Hi, I noticed that there was no answer to this question and other similar ones. I got the same problem. I am new to this area.

Thanks!
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Old 08-18-2014, 07:55 PM   #16
silverfish
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Hi,

I am a beginner, and I just downloaded and tried CONTRA before using it on my samples. I first ran the test files provided. It worked paritally until it came to the reference file part and it says:

Error: The requested fasta database file (human_g1k_v37.fasta) could not be opened. Exiting!
Creating VCF file ...
ContraTest/sampleName/table/CNATable.10rd.10bases.20bins.vcf created.
Done...

The /Table/CNATable.10rd.10bases.20bins.txt is 1.9 MB in size. The CNATable.10rd.10bases.20bins.DetailsFILTERED.txt has just the headings. The VCF file is also empty with just the headers.

I re-downloaded the fasta file and still the same error. Can someone pl. help address this? the created vcf file, ofcourse is empty.

Thanks,

Thane
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Old 11-03-2014, 06:36 AM   #17
shruti
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Default ADTex

Hi I am using ADTEx (1.0.4) but it is not running properly.
I always encounter either of the problems.
All my coordinates are in chr format for BAM, target etc files.

1.
Analysing CNV...
[1] "Analysing tumour sample with base ploidy : 3"
[1] "Analysing tumour sample with base ploidy : 2"
[1] "Analysing tumour sample with base ploidy : 4"
Error in CNA(baf$mirrored_BAF[baf$chrom == i], baf$chrom[baf$chrom == :
genomdat must be numeric
Execution halted
Error in CNA(baf$mirrored_BAF[baf$chrom == i], baf$chrom[baf$chrom == :
genomdat must be numeric
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read_file -> read.delim -> read.table -> file
In addition: Warning message:

2.
Analysing CNV...
[1] "Analysing tumour sample with base ploidy : 2"
[1][1] "Analysing tumour sample with base ploidy : 3" "Analysing tumour sample with base ploidy : 4"

Error in dnorm(x, mean, sd, log) :
Non-numeric argument to mathematical function
Calls: predict.cnv -> viterbi -> dnorm
Execution halted
Error in dnorm(x, mean, sd, log) :
Non-numeric argument to mathematical function
Calls: predict.cnv -> viterbi -> dnorm
Execution halted
Error in dnorm(x, mean, sd, log) :
Non-numeric argument to mathematical function
Calls: predict.cnv -> viterbi -> dnorm
Execution halted
Error in file(file, "rt") : cannot open the connection
Calls: read_file -> read.delim -> read.table -> file

Have any of you encountered such a problem.

Thanks

shruti
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Old 02-16-2015, 01:20 AM   #18
pmint
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Error in CNA(baf$mirrored_BAF[baf$chrom == i], baf$chrom[baf$chrom == :
genomdat must be numeric

I had same problem, and I solved.
It can be solved by adding 'mirrored_BAF' column in .baf file.
I added these command in the 147th line of cnv_analyse.R

tmp = baf$tumor_BAF
tmp[tmp > 0.5] = 1 - tmp[tmp > 0.5]
baf$mirrored_BAF = tmp

These are not so pretty, but I got results.
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Old 06-29-2015, 01:25 AM   #19
Dataman
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Quote:
Originally Posted by jtjli View Post
ADTEx is the improved version of CoNVEx

http://adtex.sourceforge.net

cheers
jason
Hi All and Jason,

I am using ADTEx to perform copy number analysis of some exome sequencing data. ADTEx requires a B-allele frequency file in order to perform ploidy estimation and genotype prediction. However, I do not know how to create such file and the ADTEx tutorial does not explain it either. I was wondering if there is a general way to create B-allele frequency files that I do not know of!

The file as is explained in the tutorial should have the following fields:

chrom - chromosome name (same format as in BED or BAM file)
SNP_loc - location of the SNP
control_BAF - B allele frequency (BAF) at each SNP in control sample
tumor_BAF - B allele frequency (BAF) at each SNP in tumor sample
control_doc - Total read count at each SNP in control sample
tumor_doc - Total read count at each SNP in tumour sample

Thank you in advance for your responses and wishing you all a nice summer.
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copy number analysis, exome sequencing, illumina, next gen sequencing, targeted resequencing

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