CONTRA cnv targeted resequencing

[m_elena_bioinfo]

Dear I'm trying to run CONTRA on my data (targeted resequencing) to detect CNV in exons. The program returns me this error:

Traceback (most recent call last):
File "contra.py", line 34, in <module>
from scripts.assign_bin_number_v2 import *
ImportError: No module named scripts.assign_bin_number_v2

The python version is 2.6.5. So I can't understand what is the error. I have installed BEDtools, R and Samtools,.
Can anyone help me?
Thanx a lot,

[Heisman]

As that just came out you may have better luck contacting the authors directly. I plan on trying it shortly but probably not for another week or two.

[jtjli]

Do you have the "scripts" directory in your contra folder? Seems like the python script cannot read that directory.

Jason

[michaelb28]

We have had some difficulties with CONTRA as well. We ran into a very similar error, so make sure that you are using versions Python2.6, R-2.13.0, and BEDTools-2.16.2. Dr. Jason Li (who I believe posted as jtjli) was very prompt and helpful via email.

[swNGS]

I second that theme, it's either the appropriate script isnt in the directory that you are running it from, or you havn't got he path to it correctly. When you get it to work it is really good... You need to make sure you have the appropriate versions of R ( that was the problem I had) and Python. Jason Li was very helpful in helping me to get it working, after which I was able to generate some very nice results. I just need to work one some R graphs to output the results....

[michaelb28]

Quick Question - Has anybody tried running CONTRA on a VM? I am running it in a Ubuntu-Linux environment, and I'm trying to find out if that may be the source of my problem. I always receive this error, even though all of my scripts are in the correct directory.

Traceback (most recent call last):
File "contra.py", line 569, in <module>
main()
File "contra.py", line 514, in main
get_genome(params.TEST, genomeFile)
File "/home/michaelb/Documents/Contra-II/CONTRA.v2.0.2/scripts/get_chr_length.py",
line 31, in get_genome
raw_header = subprocess.Popen(args, stdout =
subprocess.PIPE).communicate()[0]
File "/usr/local/lib/python2.6/subprocess.py", line 595, in __init__
errread, errwrite)
File "/usr/local/lib/python2.6/subprocess.py", line 1106, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

[swNGS]

I run it in a VM in ubuntu and have it working fine
I don't intend to keep it in the vm, but I work stuff up in a vm to avoid breaking the production machine. Also the main Linux box has the wrong Version of R o it... If you know how to get two different versions to live side by side that would be helpful....

Check your versions of python & R. Put all the scripts in the same directory as the data first off and call them from the one dir to start off with so that you can eliminate path issues

It would be helpful if you posted the commands that you ran to get that error message too

[michaelb28]

Here is the command that I ran.

{
python2.6 contra.py --target TargetSeq_Trial_Kit_Reference_target_regions_hg19.bed --test IonXpress_T_(Other file Info).bam --control IonXpress_N_(Other file Info).bam --fasta hg19.fasta --outfolder ~/Contra/Results/
}

I downloaded and installed R, Python, and BEDTools using a "sudo apt-get install" command.

For some reason the files are defaulting and installing within a usr/local/lib directory (which may have certain permissions), rather than usr/lib. I don't think CONTRA can recognize these scripts when they are within this folder. Does anyone know how to help with Python directory issues?

[jtjli]

As long as R and bedtools are available from your PATH, CONTRA will run alright..

Jason

[jtjli]

I have uploaded a new revision of CONTRA to sourceforge. Fixed some bugs, and made it compatible with the new versions of R.

Cheers
Jason

[rynrie]

I'm having trouble getting CONTRA to run on our data. I have the example files running properly, but am getting errors trying to use our own BAM files.

I used samtools sort in order to make sure they were sorted in coordinate order, but they still seem to be in a slightly different order than the example data files (eg, chrX is between chr7 and chr8). Might this be an issue? If so, I'm not sure how to get the order to match the example files.

The BAM files off an Illumina sequencer and contain short 50 bp reads. The BAM files, the BED file and the fasta all have chr*.fa notation, but I've also tried to run it with files that had the 'chr' and '.fa' removed and had no luck.

I have followed the instructions in the user guide, so have the proper versions of python, R, BEDTools, etc.

I'm at a loss as to what to try next. Help?



This is the error message:

Test file read depth = 0
Control file read depth = 0
Pre-processing Completed.
Getting the Log Ratio ...
Traceback (most recent call last):
File "contra.py", line 568, in <module>
main()
File "contra.py", line 550, in main
averageCount(testListName, controlListName, avOut, t1, n1, params.MINREADDEPTH, params.MINNBASES)
File "/home/klewis/src/CONTRA.v2.0.2/scripts/average_count.py", line 109, in averageCount
r1, r2 = getFactor(tReadCount, nReadCount)
File "/home/klewis/src/CONTRA.v2.0.2/scripts/average_count.py", line 93, in getFactor
r1 = val1/r
ZeroDivisionError: float division

[jtjli]

Hi rynrie

If you can pass me your input files (bam), i can test it out for you.

my email is jason dot li at petermac.org

Jason

[shyam_la]

Quick Question - Has anybody tried running CONTRA on a VM? I am running it in a Ubuntu-Linux environment, and I'm trying to find out if that may be the source of my problem. I always receive this error, even though all of my scripts are in the correct directory.

Traceback (most recent call last):
File "contra.py", line 569, in <module>
main()
File "contra.py", line 514, in main
get_genome(params.TEST, genomeFile)
File "/home/michaelb/Documents/Contra-II/CONTRA.v2.0.2/scripts/get_chr_length.py",
line 31, in get_genome
raw_header = subprocess.Popen(args, stdout =
subprocess.PIPE).communicate()[0]
File "/usr/local/lib/python2.6/subprocess.py", line 595, in __init__
errread, errwrite)
File "/usr/local/lib/python2.6/subprocess.py", line 1106, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Having the exact same problem. Anybody come up with a solution yet? I use Win 7 64 bit as my native OS. Hence the VM.. Also I am getting the same error when I use cygwin..

[sheenams]

Same error

Binning ...
End of assign.bin.number.py with 21417 exons in 5 bins
Significance Test ...
Process Process-3:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/genetics/bin/contra.py", line 391, in analysisPerBin
rscr = subprocess.call(args)
File "/usr/lib/python2.7/subprocess.py", line 493, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Running:
contra.py -t /home/genetics/Genomes/BED_Files/BROCA_v5_BaitTiling_bed.txt -s /home/genetics/data/LMG-240/LMG-240.chromosomeprefixes.srt.bam -c /home/genetics/Genomes/CONTRA/BROCA_v4_Contra_ref.srt.bam -f /home/genetics/Genomes/hg19_chr/human_g1k_v37.fasta -o /home/genetics/data/LMG-240/LMG-240_CONTRA

I don't think this is a PATH problem, contra.py works.
I don't think is a permission issue as /home/genetics/data/LMG-240/LMG-240_CONTRA is made, with buf and table subdirectories but those are both empty.

I'm running this in Ubuntu 12.04 in an EC2 instance on AWS.

Any one have an idea how to fix this?

[tonio100680]

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