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  • BSmooth error : File name too long

    Hi,

    I'm currently trying to run the script bsev_sort.pl from BSmooth on my data and I get the following error message:

    mkdir CA8R9ANXX_GGCTAC_L003/sorted.pre/bins/____________BC_____T_o_______A____T6____g______U_J_D_T________R___S_______3H____l02___R__4v_BwHq___________N_______v_V_______0___o_____z__m_U_____c8_____A______-m_V________J___b_____E______b___f____2______r___9____Y__9__S___M______6__r___S_9_d_H_____________d_________r__RZ___q_________r__XJ_0J-____O____L_: File name too long at bsmooth-align/bin/../lib/BtlBio/Sort/DiskSort.pm line 434.
    Child with PID 2944 exited abnormally at bsmooth-align/bin/disk_sort.pl line 167.
    Bad exit level from sort command: 512 at bsmooth-align/bin/bsev_sort.pl line 145.

    Same problem when I run it on a example data set created with sim.pl

    Any idea what's going wrong and how I can correct it ?
    Many thanks !

  • #2
    Your file name is too long. Shorten it? Where is that underscore based hell being derived from? If it's coming from the temporary data directory creation try specify a tempdir at execution
    Last edited by Bukowski; 08-20-2018, 03:32 AM.

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    • #3
      Thank you for your reply. The problem is that the files in sorted.pre/bins/ are temporary files created by the script, so I don't control it.

      Comment


      • #4
        Are you running under a job scheduler? I just tried to run the tests, but merman doesn't seem to compile under g++ 5.5.0 - and in fact there's an open issue on that repo that's 3.5 years old, which implies this package is no longer maintained.

        Comment


        • #5
          Yes, I'm using a pbs server.
          I will find another way to process my data,
          Thank you for your time !

          Comment

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