cuffdiff question

[jlfmssm]

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