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Old 01-15-2014, 04:40 AM   #21
wolfpack14
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Found another bug. If CONTRA runs and forces you data into 1 bin, you must launch CONTRA with the option --numBin 1. If you don't, the application will fail.

It is a bug in how cn_analysis.v3.R handles bin sizes of 1. It doesn't carry over the actual bin size of your data, but rather the specified bin size from the application launch (20 by default).
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Old 01-27-2014, 10:04 AM   #22
wolfpack14
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cecile,

I think your BAM files are too large. I am successfully running CONTRA on BAM files that are about 200-300MB. How big are the bins in your target BED file? That may also make a difference in performance.
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Old 01-28-2014, 04:06 AM   #23
cecile75
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Hi wolfpack14,

Indeed, my bam files are ~18 Ga.
The intervals in my target BED file vary from 200bp to 1000 bp. I did'nt specify the option --nomBin, so I ran CONTRA with the default (20).

I ran it after spliting my bam files by chromosome (using Bamtools split), and it also failed. The error was about the bam file, which seemed to be malformed.

I did another test by spliting the file with samtools view -bh file.bam chr${num} and it worked.
But it seems there is no significant result (nothing in CNATable.10rd.10bases.20bins.DetailsFILTERED) althougt there were 6439 targets.
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Old 01-28-2014, 06:23 AM   #24
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Have you tried playing around with the minExon setting? We have ours set at 100 so we can make appropriate bin sizes. If we left it at 2000 (the default), CONTRA had a tough time splitting the data up into enough bins.

We also forced our input BED intervals to width 20. We are getting pretty granular results from this combination.
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Old 01-30-2014, 09:42 AM   #25
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Just solved another issue we were having with using multiple input bed files on a CONTRA built baseline....

You have to build a new baseline for each input bed you want to use. CONTRA will only work if the input bed file matches the one used to create the original baseline. I think it has to do with non-matching base pair intervals. I kept getting "list out of index" errors on the control sample.

Last edited by wolfpack14; 01-30-2014 at 09:45 AM. Reason: Grammar
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Old 01-30-2014, 09:47 AM   #26
wolfpack14
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Cecile,

I think you forgot to specify that your input file is in BED format. I can tell because your output has this:

Quote:
bedInput : False
Use the --bed parameter when you launch CONTRA. I think it will solve your problem.

If it doesn't solve your issue, try running without the -l option (CBS Large Variation detection). That is probably what is taking so long.

Last edited by wolfpack14; 01-30-2014 at 09:53 AM. Reason: Added Info
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Old 01-31-2014, 05:30 AM   #27
nielsk
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Hi,

Im trying to get CONTA working.
However, using the testfiles i get the following error:
Quote:
DEBUG 266b

fastaFromBed -fi reference/human_g1k_v37.fasta -bed testfix2/buf/CNATable.10rd.10bases.20bins.BED -fo testfix2/buf/CNATable.10rd.10bases.20bins.fastaOut.txt -name
Error: The requested bed file (testfix2/buf/CNATable.10rd.10bases.20bins.BED) could not be opened. Exiting!
Creating VCF file ...
testfix2/table/CNATable.10rd.10bases.20bins.vcf created.
Done...
Command used:
Quote:
python CONTRA.v2.0.4/contrafix.py -t test_files/0247401_D_BED_20090724_hg19_MERGED.bed -s test_files/P0667T_GATKrealigned_duplicates_marked.bam -c test_files/P0667N_GATKrealigned_duplicates_marked.bam -f reference/human_g1k_v37.fasta -o testfix2

I was wondering if someone could help me to solve this error.

I am planning to determine CNV on IonTorrent PGM data.
Do you think CONTRA would be suitable for this?
Or do you suggest another program?

Nevertheless, I hope someone can help me to fix this!

Thanks in advance
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Old 02-04-2014, 04:53 AM   #28
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Are there still people using CONTRA?
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Old 11-13-2014, 06:49 AM   #29
dnusol
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Hi nielsk,

are you still running into this error?

If so, I am just trying out CONTRA for the first time so this may be of no help to you.

It seems CONTRA cannot find your .bed file in testfix2/buf/ directory. Can you check your paths are correct? You seem to be executing CONTRA from your home dir or something similar and you have also your test files and your reference in the same directory

From my initial tests, CONTRA copies your target bed file to the buf directory and renames it target.BED

But in your case CONTRA seems to be looking for the original name of the file. I wonder if copying the file manually into the buf directory will make the trick

Anyway, have you managed to get any CNV results from your PGM data? it would be interesting to know if it works on single-end reads with a targeted resequencing experiment

HTH

Dave

Last edited by dnusol; 11-13-2014 at 06:52 AM.
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Old 08-14-2015, 01:11 PM   #30
DNAmethylome
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Hi Dr. Li,

I have some problems running CONTRA, and I have posted a thread here:
http://seqanswers.com/forums/showthread.php?t=62000

Could you please help me on that?

Thanks a lot!

-J
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Old 08-14-2015, 01:16 PM   #31
DNAmethylome
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Default CONTRA error messages

Quote:
Originally Posted by jtjli View Post
Do you have the "scripts" directory in your contra folder? Seems like the python script cannot read that directory.

Jason
Hi Dr. Li,

I have some problems running CONTRA, I have posted a thread here:
http://seqanswers.com/forums/showthread.php?t=62000

Could you please help me on that?

Thanks a lot!

-J
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Old 08-26-2015, 01:23 PM   #32
xxqtony
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I tried to run CONTRA v2.0.6 and eventually got it run, but it seems to hang over there for half an hour for a pair of 1.3M sample and 0.8M control bam files. Here is the output I got on the screen. Anyone has clue why?

./contra.py --target target_test.bed -s bamfiles/Sample.32.NA18924.3cp.bam -c bamfiles/Control.75.NA19351.bam -f /share/references/hg19/hg19.fa -o out.run
target : target_test.bed
test : bamfiles/Sample.32.NA18924.3cp.bam
control : bamfiles/Control.75.NA19351.bam
fasta : /share/references/hg19/hg19.fa
outfolder : out.run
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
Converting TEST Sample...
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam bamfiles/Sample.32.NA18924.3cp.bam -bga -g out.run/buf/sample.Genome
DEBUG 123 genomeCoverageBed -ibam bamfiles/Control.75.NA19351.bam -bga -g out.run/buf/sample.Genome
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Test file read depth = 230090
Control file read depth = 155939
Pre-processing Completed.
Getting the Log Ratio ...
Binning ...
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Old 08-26-2015, 01:27 PM   #33
DNAmethylome
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Hi,

What is your python version?

Quote:
Originally Posted by xxqtony View Post
I tried to run CONTRA v2.0.6 and eventually got it run, but it seems to hang over there for half an hour for a pair of 1.3M sample and 0.8M control bam files. Here is the output I got on the screen. Anyone has clue why?

./contra.py --target target_test.bed -s bamfiles/Sample.32.NA18924.3cp.bam -c bamfiles/Control.75.NA19351.bam -f /share/references/hg19/hg19.fa -o out.run
target : target_test.bed
test : bamfiles/Sample.32.NA18924.3cp.bam
control : bamfiles/Control.75.NA19351.bam
fasta : /share/references/hg19/hg19.fa
outfolder : out.run
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
Converting TEST Sample...
Converting CONTROL Sample...
DEBUG 123 genomeCoverageBed -ibam bamfiles/Sample.32.NA18924.3cp.bam -bga -g out.run/buf/sample.Genome
DEBUG 123 genomeCoverageBed -ibam bamfiles/Control.75.NA19351.bam -bga -g out.run/buf/sample.Genome
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Getting targeted regions DOC...
chr22
Targeted regions pre-processing: Done
Test file read depth = 230090
Control file read depth = 155939
Pre-processing Completed.
Getting the Log Ratio ...
Binning ...
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Old 08-26-2015, 01:55 PM   #34
xxqtony
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I also got errors when I use the provided testing files (at sourceforge dot net contra-cnv testing files folder). I used the command in README file, screen output copied below:

~/programs/CONTRA.v2.0.6/contra.py -t 0247401_D_BED_20090724_hg19_MERGED.bed -s P0667T_GATKrealigned_duplicates_marked.bam -c P0667N_GATKrealigned_duplicates_marked.bam -f /share/references/hg19/human_g1k_v37.fasta -o P0667Test
target : 0247401_D_BED_20090724_hg19_MERGED.bed
test : P0667T_GATKrealigned_duplicates_marked.bam
control : P0667N_GATKrealigned_duplicates_marked.bam
fasta : /share/references/hg19/human_g1k_v37.fasta
outfolder : P0667Test
numBin : [20]
minreaddepth : 10
minNBases : 10
sam : False
pval : 0.05
sampleName : No-SampleName
nomultimapped : False
plot : False
bedInput : False
minExon : 2000
largeDeletion : False
removeDups : False
Creating Output Folder : Done.
begining to sort 0247401_D_BED_20090724_hg19_MERGED.bed into?
[bam_header_read] EOF marker is absent. The input is probably truncated.
Converting TEST Sample...
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
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
WARNING: P0667Test/buf/testData/chr/chr16.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr16), in turn likely due to currupted bam files
chr17
WARNING: P0667Test/buf/testData/chr/chr17.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr17), in turn likely due to currupted bam files
chr18
WARNING: P0667Test/buf/testData/chr/chr18.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr18), in turn likely due to currupted bam files
chr19
WARNING: P0667Test/buf/testData/chr/chr19.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr19), in turn likely due to currupted bam files
chr2
chr20
WARNING: P0667Test/buf/testData/chr/chr20.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr20), in turn likely due to currupted bam files
chr21
WARNING: P0667Test/buf/testData/chr/chr21.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr21), in turn likely due to currupted bam files
chr22
WARNING: P0667Test/buf/testData/chr/chr22.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chr22), in turn likely due to currupted bam files
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
WARNING: P0667Test/buf/testData/chr/chrX.txt NOT FOUND (should be generated by splitByChromosome3). Likely due to no reads found in a targeted chromosome (chrX), in turn likely due to currupted bam files
Targeted regions pre-processing: Done
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
Targeted regions pre-processing: Done
Test file read depth = 227284587
Control file read depth = 304798449
Pre-processing Completed.
Getting the Log Ratio ...
Initial: 5292
Check_Init.id: 3021
_Exon: 0
Check_Init.exon: 0
Error. Comparing different Gene



BTW, I'm using python 2.7.6 and R 3.2.1
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Old 12-14-2015, 10:40 AM   #35
aditisk
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I am trying to run Contra with the test data provided. I am using the Nimblegen V2 baseline file that is provided and I am running into this error:

Process Process-2:
Traceback (most recent call last):
File "/home/software/rhel6/python/2.7.3/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/home/software/rhel6/python/2.7.3/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/software/rhel6/med/contra/2.0.6/contra.py", line 345, in convertBamSimple
convertGeneCoordinate(targetList, folder)
File "/usr/cac/rhel6/med/contra/2.0.6/scripts/convert_gene_coordinate.py", line 77, in convertGeneCoordinate
cov = covFile[t].split()
IndexError: list index out of range
Traceback (most recent call last):
File "/home/software/rhel6/med/contra/2.0.6/contra.py", line 613, in <module>
main()
File "/home/software/rhel6/med/contra/2.0.6/contra.py", line 585, in main
n1 = int(file.readlines(open(folder+"temp.txt"))[0].strip("\n"))
IOError: [Errno 2] No such file or directory: '/scratch/chadbren_flux/aditisk/Bam/Contra_Out/Sample_Baseline/buf/ctrData/temp.txt'

Does anyone have an idea as to what might be the problem ?

Thanks,
Aditi
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