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  • Cuffnorm "killed" error

    Hello wise people

    I am trying to run the cufflinks->cuffmerge->cuffquant->cuffnorm pipeline (Cufflinks 2.2.1) on ~300 samples. The first 3 steps worked fine, and there is one merged gtf file and ~300 .cxb files.
    Now I am trying to run cuffnorm:
    $ cuffnorm -p 8 -o HypoTsamples --use-sample-sheet $CUFFGTF CXB_samples.txt

    This produces the following behavior:
    "You are using Cufflinks v2.2.1, which is the most recent release.
    [17:48:10] Loading reference annotation.
    Killed " <- about an hour later

    Running cuffnorm with small subset of the CXB_samples.txt works just fine (takes ~10 minutes for 6 samples).

    head of CXB_samples.txt looks like this:

    sample_id group_id
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoT129X1zSvJzOBz1301/abundances.cxb HypoT129X1zSvJzOBz1301
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoT129X1zSvJzOBz1302/abundances.cxb HypoT129X1zSvJzOBz1302
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoT129X1zSvJzOBz1303/abundances.cxb HypoT129X1zSvJzOBz1303
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoTAKRzJzOBz1398/abundances.cxb HypoTAKRzJzOBz1398
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoTAKRzJzOBz1399/abundances.cxb HypoTAKRzJzOBz1399
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoTAKRzJzOBz1400/abundances.cxb HypoTAKRzJzOBz1400
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoTAXB12zPgnJzOBz1346/abundances.cxb HypoTAXB12zPgnJzOBz1346
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoTAXB13zPgnJzOBz1387/abundances.cxb HypoTAXB13zPgnJzOBz1387
    /u/scratch/y/yhasin/Hypo_SampleBAM/1_CuffQuant/HypoTAXB13zPgnJzOBz1388/abundances.cxb HypoTAXB13zPgnJzOBz1388

    Do you know if there a limit on number of samples for cuffnorm - either by the program ? Is it memory or number of processors issue (I can increase both if needed)?

    What would be the best way to run it on more than the maximum number of samples - what should be the size of a data set? How many samples should overlap between them to get consistent fpkm estimates?

    Best,
    Yehudit
    Yu

  • #2
    Usually "Killed" means that your computer killed the process, often due to using all of the RAM.

    Comment


    • #3
      Hi Devon
      Thanks for the answer. I thought so too, but why would it have enough RAM to load the annotation for 6 samples, but not for 300? Its the same annotation. I wish there would be some more detailed description what exactly the programs do in each step....

      Yu
      Yu

      Comment

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