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  • question about cuffdiff

    I am trying to run cuffdiff like the following:

    /cluster2/aimin/cufflinks-0.8.3-1309/bin/cuffdiff -m 50 /cluster2/aimin/MGED_13/ensemble_snippet.gtf /cluster2/aimin/MGED_13/bowtie_indexes/exp_tophat_out/accepted_hits.sam /cluster2/aimin/MGED_13/bowtie_indexes/60hr_tophat_out/accepted_hits.sam /cluster2/aimin/MGED_13/bowtie_indexes/5day_tophat_out/accepted_hits.sam /cluster2/aimin/MGED_13/bowtie_indexes/7day_tophat_out/accepted_hits.sam

    my output should be /cluster2/aimin/MGED_13/bowtie_indexes(see below)

    [aimin@freesia bowtie_indexes]$ pwd
    /cluster2/aimin/MGED_13/bowtie_indexes
    [aimin@freesia bowtie_indexes]$ ls -al
    total 322028
    drwxr-xr-x 6 aimin stats 4096 Jul 15 10:56 .
    drwxr-xr-x 3 aimin stats 4096 Jul 14 23:08 ..
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_cds.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_cds_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_gene_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_isoform_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_promoters.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_splicing.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 0_1_tss_group_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_cds.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_cds_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_gene_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_isoform_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_promoters.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_splicing.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 1_2_tss_group_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_cds.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_cds_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_gene_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_isoform_exp.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_promoters.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_splicing.diff
    -rw------- 1 aimin stats 0 Jul 14 23:59 2_3_tss_group_exp.diff
    drwx------ 3 aimin stats 4096 Jul 14 23:44 5day_tophat_out
    drwx------ 3 aimin stats 4096 Jul 14 23:43 60hr_tophat_out
    drwx------ 3 aimin stats 4096 Jul 14 23:45 7day_tophat_out
    -rw------- 1 aimin stats 0 Jul 14 23:59 cds.fpkm_tracking
    -rw-r--r-- 1 aimin stats 47591182 Jun 24 22:38 chr4.1.ebwt
    -rw-r--r-- 1 aimin stats 18985860 Jun 24 22:38 chr4.2.ebwt
    -rw-r--r-- 1 aimin stats 287 Jun 24 22:38 chr4.3.ebwt
    -rw-r--r-- 1 aimin stats 37971711 Jun 24 22:38 chr4.4.ebwt
    -rw-r--r-- 1 aimin stats 158223962 Jul 14 23:20 chr4.fa
    -rw-r--r-- 1 aimin stats 47591182 Jun 24 22:38 chr4.rev.1.ebwt
    -rw-r--r-- 1 aimin stats 18985860 Jun 24 22:38 chr4.rev.2.ebwt
    -rw------- 1 aimin stats 6096 Jul 14 23:58 errorfile_top
    drwx------ 3 aimin stats 4096 Jul 14 23:35 exp_tophat_out
    -rw------- 1 aimin stats 0 Jul 14 23:59 genes.fpkm_tracking
    -rw------- 1 aimin stats 0 Jul 14 23:59 isoforms.fpkm_tracking
    -rw------- 1 aimin stats 0 Jul 14 23:55 outputfile_top
    -rw------- 1 aimin stats 0 Jul 14 23:59 tss_groups.fpkm_tracking

    but after runing the whole night, those output files are still empty, cuffdiff is still runing.


    I am not sure if this is ok, Does anyone know how long it takes for cuffdiff to finish their job.

    Thanks,

    jlm

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