Question: Any One Has Sucess With Cuffdiff With Gencode V16 Or V15 Gtf File?
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gravatar for Rm
6.8 years ago by
Rm7.9k
Danville, PA
Rm7.9k wrote:

Similar to this Question: cufflinks segmentation fault

I ran latest cuffdiff on just a pair of samples using Gencode_v16 (tried V15 too) encountering segmentation fault. But with ensemble gtf its working fine.

I need your suggestions to trouble shoot this issue.

Command used and error message:

/tools/cufflinks-2.1.1.Linux_x86_64/cuffdiff -o /scratch/control-case  --no-update-check --num-threads 16 --multi-read-correct --frag-bias-correct /scratch/human_g1k_v37.fa -L control,case -M /scratch/gencode.v16.annotation.Mt.rRNA.MASK.gtf /scratch/gencode.v16.annotation.gtf /scratch/tophat_SpinalCord_Control/accepted_hits.bam /scratch/tophat_SpinalCord_Case/accepted_hits.bam

[13:42:12] Loading reference annotation and sequence.
[13:43:43] Loading reference annotation.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[13:43:44] Inspecting maps and determining fragment length distributions.
[14:15:02] Modeling fragment count overdispersion.
> Map Properties:
>       Normalized Map Mass: 46524781.92
>       Raw Map Mass: 30653024.19
>       Number of Multi-Reads: 990850 (with 2569329 total hits)
>       Fragment Length Distribution: Empirical (learned)
>                     Estimated Mean: 154.62
>                  Estimated Std Dev: 61.38
> Map Properties:
>       Normalized Map Mass: 46524781.92
>       Raw Map Mass: 69511626.23
>       Number of Multi-Reads: 2429303 (with 6034463 total hits)
>       Fragment Length Distribution: Empirical (learned)
>                     Estimated Mean: 158.98
>                  Estimated Std Dev: 65.56
[14:16:45] Calculating preliminary abundance estimates
.................
> Processing Locus 1:47223509-47285085         [                         ]   2%
> Processing Locus 1:48671636-48672515         [                         ]   2%
> Processing Locus 1:48630300-48648100         [                         ]   2%
> Processing Locus 1:47799468-47844511         [                         ]   2%
> Processing Locus 1:48962934-48963408         [                         ]   2%/cm/local/apps/torque/var/spool/mom_priv/jobs/6360.cluster.SC: line 63:  8285 Segmentation fault      (core dumped)
cuffdiff • 2.5k views
ADD COMMENTlink modified 6 months ago by chenlin_9200 • written 6.8 years ago by Rm7.9k

I also got the same problem and couldn't found the solution. Any advice would be welcome.

ADD REPLYlink written 6 months ago by chenlin_9200
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