Question: Cuffdiff error- Fatal error: Exit code 139 ()
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gravatar for bioananthi.08
7 months ago by
bioananthi.080 wrote:

Hi, I am getting the following error while running Galaxy cuff diff.

An error occured with this dataset: Fatal error: Exit code 139 () Loading reference annotation and sequence. Warning: No conditions are replicated, switching to blind dispersion method. Inspecting maps and determing fragment length distributions. Modelin

Dataset generation errors Dataset 1080: cuffdiff on data 937, data 872, and others: gene FPKM tracking Tool execution generated the following error message:

Fatal error: Exit code 139 () [01:20:20] Loading reference annotation and sequence. Warning: No conditions are replicated, switching to 'blind' dispersion method [01:20:49] Inspecting maps and determining fragment length distributions. [01:29:03] Modeling fragment count overdispersion.

Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 15718675.67 Fragment Length Distribution: Empirical (learned) Estimated Mean: 164.52 Estimated Std Dev: 60.35 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 14355555.23 Fragment Length Distribution: Empirical (learned) Estimated Mean: 153.94 Estimated Std Dev: 62.53 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 19233427.96 Fragment Length Distribution: Empirical (learned) Estimated Mean: 160.84 Estimated Std Dev: 61.91 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 11984408.57 Fragment Length Distribution: Empirical (learned) Estimated Mean: 173.98 Estimated Std Dev: 62.72 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 5701271.99 Fragment Length Distribution: Empirical (learned) Estimated Mean: 161.39 Estimated Std Dev: 57.63 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 18812039.37 Fragment Length Distribution: Empirical (learned) Estimated Mean: 173.36 Estimated Std Dev: 63.23 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 11142365.17 Fragment Length Distribution: Empirical (learned) Estimated Mean: 170.92 Estimated Std Dev: 60.27 Map Properties: Normalized Map Mass: 11742681.08 Raw Map Mass: 6019430.53 Fragment Length Distribution: Empirical (learned) Estimated Mean: 168.31 Estimated Std Dev: 63.81 [01:33:46] Calculating preliminary abundance estimates Processed 20089 loci.
[02:54:41] Learning bias parameters. [03:06:59] Testing for differential expression and regulation in locus. /galaxy-repl/main/jobdir/016/186/16186091/tool_script.sh: line 9: 9926 Segmentation fault (core dumped) cuffdiff --no-update-check --quiet --FDR=0.05 --num-threads="${GALAXY_SLOTS:-4}" --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=blind -b "/galaxy/data/hg19/sam_index/hg19.fa" --labels 'Control_1','Control_2','Control_3','Control_4','Test_1','Test_2','Test_3','Test_4' /galaxy-repl/main/files/019/724/dataset_19724831.dat /galaxy-repl/main/files/019/163/dataset_19163323.dat /galaxy-repl/main/files/019/275/dataset_19275571.dat /galaxy-repl/main/files/019/344/dataset_19344813.dat /galaxy-repl/main/files/019/709/dataset_19709135.dat /galaxy-repl/main/files/019/163/dataset_19163306.dat /galaxy-repl/main/files/019/319/dataset_19319579.dat /galaxy-repl/main/files/019/349/dataset_19349260.dat /galaxy-repl/main/files/019/709/dataset_19709545.dat

(Dataset information 8 sets, 4 sets of control and 4 sets of test.
Dispersion method-blind)

This same dataset I successfully ran before a month without any error. Now am getting error in all cuffdiff set, So,I just gave re-run option I got the above mentioned error.

Can you please tell me about this error

Thank you in advance.

rna-seq galaxy • 217 views
ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson24k • written 7 months ago by bioananthi.080
0
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Please rerun now. This was most likely a cluster error. I see the prior failed/success jobs in your histories at http://usegalaxy.org and this was the prior reason for the same problems.

Sorry for the inconvenience, Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson24k
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