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  • #16
    Hi,
    I am having exactly the same problem. The .txt RPKM files that are generated are empty. I have indexed all my BAM files and I'm giving the complete path for all my files in the command.
    What might be going wrong?

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    • #17
      I figured out why my rpkm files were blank and it turns out that my BAM index files are not being recognized even though they are in the same folder as my BAM files.

      I don't know why it is unable to find the BAM index files

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      • #18
        Originally posted by aditisk View Post
        I figured out why my rpkm files were blank and it turns out that my BAM index files are not being recognized even though they are in the same folder as my BAM files.

        I don't know why it is unable to find the BAM index files
        Did you generate your bam file using GAKT? The index file should have the extention *.bam.bai no just *.bai as outputted by GATK.

        You can just copy the *.bai file to *.bam.bai and it should work.

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        • #19
          I realize this is an outdated thread but I am trying to run CONIFER for the first time and having some issues. I cannot run the very first command to generate the RPKM files. Like someone said above, my files are just blank. When I run it in python I get the error:

          “Segmentation fault (core dumped)”

          I don't know what the source of the error or what it means. I was wondering if it was a memory issue because the bam files that I am trying to read in are ~20GB. I don't know what size files others in this thread are dealing with. I also read about the issue with the index files not matching but I fixed that cause I ran into the same problem with another CNV detection program. Any help would be greatly appreciated.

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