Question: please help its the final step and got Cuffdiff error
1
gravatar for Fat.eldefrawy
5 months ago by
USA
Fat.eldefrawy10 wrote:

Hello everyone, I'm very new in RNA seq analysis I have run cuffdiff on 3 condition dataset collections( control and 2 different treatment groups) using GALAXY, then I got an error, I have repeated the same job many times, unfortunately, I got the same result.

Fatal error: Exit code 1 () 
[04:06:22] Loading reference annotation.
[04:06:23] Inspecting maps and determining fragment length distributions. 
[04:30:24] Modeling fragment count overdispersion.
[04:32:50] Modeling fragment count overdispersion. 
[04:35:14

I also tried to use annotation file (GTF) of the same genome build I have used in cufflink instead of cuffmerge transcriptome GTF file but got the same problem

Any help will be appreciated. Regards

(admin edit: reformat post text)

ADD COMMENTlink modified 5 months ago • written 5 months ago by Fat.eldefrawy10
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The inputs look fine. The problem is with using the SQLite optional output. This function is problematic at Galaxy Main https://usegalaxy.org right now.

Please see the issue ticket describing the problem and a workaround. Updates for the correction will also post back to this ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/50

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k

I have tried to deselect SQLite optional output. but still facing the same problem, I sent a bug report but really I couldn't understand what error information means, I don't have any experience on the command line, please check that

Job Execution and Failure Information Command Line cuffdiff --no-update-check --quiet --FDR=0.05 --num-threads="${GALAXY_SLOTS:-4}" --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled --labels 'VH','BA','BS' '/galaxy-repl/main/files/024/819/dataset_24819040.dat' '/galaxy-repl/main/files/024/789/dataset_24789405.dat,/galaxy-repl/main/files/024/789/dataset_24789410.dat,/galaxy-repl/main/files/024/789/dataset_24789415.dat,/galaxy-repl/main/files/024/789/dataset_24789420.dat' '/galaxy-repl/main/files/024/789/dataset_24789431.dat,/galaxy-repl/main/files/024/789/dataset_24789436.dat,/galaxy-repl/main/files/024/789/dataset_24789441.dat,/galaxy-repl/main/files/024/789/dataset_24789446.dat' '/galaxy-repl/main/files/024/789/dataset_24789473.dat,/galaxy-repl/main/files/024/789/dataset_24789479.dat,/galaxy-repl/main/files/024/789/dataset_24789484.dat,/galaxy-repl/main/files/024/789/dataset_24789489.dat'

ADD REPLYlink written 5 months ago by Fat.eldefrawy10
0
gravatar for Fat.eldefrawy
5 months ago by
USA
Fat.eldefrawy10 wrote:

I have tried to deselect SQLite optional output. but still facing the same problem, I sent a bug report but really I couldn't understand what error information means, I don't have any experience on the command line, please check that

Job Execution and Failure Information Command Line cuffdiff --no-update-check --quiet --FDR=0.05 --num-threads="${GALAXY_SLOTS:-4}" --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled --labels 'VH','BA','BS' '/galaxy-repl/main/files/024/819/dataset_24819040.dat' '/galaxy-repl/main/files/024/789/dataset_24789405.dat,/galaxy-repl/main/files/024/789/dataset_24789410.dat,/galaxy-repl/main/files/024/789/dataset_24789415.dat,/galaxy-repl/main/files/024/789/dataset_24789420.dat' '/galaxy-repl/main/files/024/789/dataset_24789431.dat,/galaxy-repl/main/files/024/789/dataset_24789436.dat,/galaxy-repl/main/files/024/789/dataset_24789441.dat,/galaxy-repl/main/files/024/789/dataset_24789446.dat' '/galaxy-repl/main/files/024/789/dataset_24789473.dat,/galaxy-repl/main/files/024/789/dataset_24789479.dat,/galaxy-repl/main/files/024/789/dataset_24789484.dat,/galaxy-repl/main/files/024/789/dataset_24789489.dat'

ADD COMMENTlink written 5 months ago by Fat.eldefrawy10

stderr Fatal error: [23:13:23] Loading reference annotation. [23:13:23] Inspecting maps and determining fragment length distributions. [23:35:43] Modeling fragment count overdispersion. [23:38:00] Modeling fragment count overdispersion. [23:40:24] Modeling fragment count overdispersion.

Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3495302.83 Fragment Length Distribution: Empirical (learned) Estimated Mean: 202.52 Estimated Std Dev: 44.72 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3383043.21 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.51 Estimated Std Dev: 44.06 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3904499.36 Fragment Length Distribution: Empirical (learned) Estimated Mean: 202.72 Estimated Std Dev: 45.10 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3574743.50 Fragment Length Distribution: Empirical (learned) Estimated Mean: 203.00 Estimated Std Dev: 45.56 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 2943496.77 Fragment Length Distribution: Empirical (learned) Estimated Mean: 204.11 Estimated Std Dev: 46.06 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3153977.63 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.76 Estimated Std Dev: 44.87 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3232598.92 Fragment Length Distribution: Empirical (learned) Estimated Mean: 200.20 Estimated Std Dev: 43.72 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3174491.54 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.21 Estimated Std Dev: 43.80 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3573090.35 Fragment Length Distribution: Empirical (learned) Estimated Mean: 204.14 Estimated Std Dev: 45.50 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3158465.26 Fragment Length Distribution: Empirical (learned) Estimated Mean: 199.62 Estimated Std Dev: 41.75 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3641930.62 Fragment Length Distribution: Empirical (learned) Estimated Mean: 200.55 Estimated Std Dev: 43.12 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3020355.14 Fragment Length Distribution: Empirical (learned) Estimated Mean: 204.11 Estimated Std Dev: 45.62 [23:42:49] Calculating preliminary abundance estimates [23:42:49] Testing for differential expression and regulation in locus. PCDHA1 PCDHA4 PCDHA1 PCDHA12 PCDHA7 PCDHA9 PCDHA11 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA8 PCDHA1 PCDHA4 PCDHA1 PCDHA12 PCDHA7 PCDHA9 PCDHA11 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA8 PCDHA1 PCDHA4 PCDHA1 PCDHA12 PCDHA7 PCDHA9 PCDHA11 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA8 SLC22A4 SLC22A5 SLC22A4 SLC22A5 SLC22A4 SLC22A5 LOC768350 MR1 LOC768350 MR1 LOC768350 MR1 PCDHA1 PCDHA11 PCDHA2 PCDHA3 PCDHA5 PCDHA8 PCDHA9 PCDHA1 PCDHA11 PCDHA2 PCDHA3 PCDHA5 PCDHA8 PCDHA9 PCDHA1 PCDHA11 PCDHA2 PCDHA3 PCDHA5 PCDHA8 PCDHA9 Processed 6375 loci. Performed 14214 isoform-level transcription difference tests Performed 13991 tss-level transcription difference tests Performed 13705 gene-level transcription difference tests Performed 14027 CDS-level transcription difference tests Performed 210 splicing tests Performed 141 promoter preference tests Performing 222 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking Writing isoform-level count tracking Writing TSS group-level count tracking Writing gene-level count tracking Writing CDS-level count tracking Writing isoform-level read group tracking Writing TSS group-level read group tracking Writing gene-level read group tracking Writing CDS-level read group tracking Writing read group info Writing run info slurmstepd: error: Detected 1 oom-kill event(s) in step 13341424.batch cgroup.

ADD REPLYlink written 5 months ago by Fat.eldefrawy10
0
gravatar for Fat.eldefrawy
5 months ago by
USA
Fat.eldefrawy10 wrote:

stderr Fatal error: [23:13:23] Loading reference annotation. [23:13:23] Inspecting maps and determining fragment length distributions. [23:35:43] Modeling fragment count overdispersion. [23:38:00] Modeling fragment count overdispersion. [23:40:24] Modeling fragment count overdispersion.

Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3495302.83 Fragment Length Distribution: Empirical (learned) Estimated Mean: 202.52 Estimated Std Dev: 44.72 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3383043.21 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.51 Estimated Std Dev: 44.06 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3904499.36 Fragment Length Distribution: Empirical (learned) Estimated Mean: 202.72 Estimated Std Dev: 45.10 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3574743.50 Fragment Length Distribution: Empirical (learned) Estimated Mean: 203.00 Estimated Std Dev: 45.56 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 2943496.77 Fragment Length Distribution: Empirical (learned) Estimated Mean: 204.11 Estimated Std Dev: 46.06 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3153977.63 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.76 Estimated Std Dev: 44.87 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3232598.92 Fragment Length Distribution: Empirical (learned) Estimated Mean: 200.20 Estimated Std Dev: 43.72 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3174491.54 Fragment Length Distribution: Empirical (learned) Estimated Mean: 201.21 Estimated Std Dev: 43.80 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3573090.35 Fragment Length Distribution: Empirical (learned) Estimated Mean: 204.14 Estimated Std Dev: 45.50 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3158465.26 Fragment Length Distribution: Empirical (learned) Estimated Mean: 199.62 Estimated Std Dev: 41.75 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3641930.62 Fragment Length Distribution: Empirical (learned) Estimated Mean: 200.55 Estimated Std Dev: 43.12 Map Properties: Normalized Map Mass: 3340514.94 Raw Map Mass: 3020355.14 Fragment Length Distribution: Empirical (learned) Estimated Mean: 204.11 Estimated Std Dev: 45.62 [23:42:49] Calculating preliminary abundance estimates [23:42:49] Testing for differential expression and regulation in locus. PCDHA1 PCDHA4 PCDHA1 PCDHA12 PCDHA7 PCDHA9 PCDHA11 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA8 PCDHA1 PCDHA4 PCDHA1 PCDHA12 PCDHA7 PCDHA9 PCDHA11 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA8 PCDHA1 PCDHA4 PCDHA1 PCDHA12 PCDHA7 PCDHA9 PCDHA11 PCDHA13 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA8 SLC22A4 SLC22A5 SLC22A4 SLC22A5 SLC22A4 SLC22A5 LOC768350 MR1 LOC768350 MR1 LOC768350 MR1 PCDHA1 PCDHA11 PCDHA2 PCDHA3 PCDHA5 PCDHA8 PCDHA9 PCDHA1 PCDHA11 PCDHA2 PCDHA3 PCDHA5 PCDHA8 PCDHA9 PCDHA1 PCDHA11 PCDHA2 PCDHA3 PCDHA5 PCDHA8 PCDHA9 Processed 6375 loci.
Performed 14214 isoform-level transcription difference tests Performed 13991 tss-level transcription difference tests Performed 13705 gene-level transcription difference tests Performed 14027 CDS-level transcription difference tests Performed 210 splicing tests Performed 141 promoter preference tests Performing 222 relative CDS output tests Writing isoform-level FPKM tracking Writing TSS group-level FPKM tracking Writing gene-level FPKM tracking Writing CDS-level FPKM tracking Writing isoform-level count tracking Writing TSS group-level count tracking Writing gene-level count tracking Writing CDS-level count tracking Writing isoform-level read group tracking Writing TSS group-level read group tracking Writing gene-level read group tracking Writing CDS-level read group tracking Writing read group info Writing run info slurmstepd: error: Detected 1 oom-kill event(s) in step 13341424.batch cgroup.

any suggestion will help Fat

ADD COMMENTlink written 5 months ago by Fat.eldefrawy10
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