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  • 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.

  • #2
    CONTRA.v2.0.3 is now available on sourceforge. Fixed some bugs, and it is now compatible with the new versions of R.

    Comment


    • #3
      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.

      Comment


      • #4
        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

        Comment


        • #5
          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.
          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

          Comment


          • #6
            And when I say that the vcf file is empty, I mean that there is only the header...!

            Comment


            • #7
              I am encountering the same problem as jmatés. 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!

              Comment


              • #8
                What about CoNVex? How come I couldn't find anywhere to download the program?

                Comment


                • #9
                  ADTEx is the improved version of CoNVEx



                  cheers
                  jason

                  Comment


                  • #10
                    Originally posted by jtjli View Post
                    Thanks a lot for your reply. I will give it a try.

                    Comment


                    • #11
                      Originally posted by jtjli View Post
                      Wow. This program is very user friendly compare to Control-FREEC or ExomeCNV.

                      What about tumor purity estimation? Is it done internally?

                      Comment


                      • #12
                        Originally posted by jtjli View Post
                        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, 05:22 PM.

                        Comment


                        • #13
                          Originally posted by gary View Post
                          I am encountering the same problem as jmatés. 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...

                          Comment


                          • #14
                            Can ADTex be used for finding CNVs for normal tissue? If not, what is the best tool for that? Thanks

                            Comment


                            • #15
                              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!

                              Comment

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