Hi
I am trying to run cuffdiff after running cuffmerge but everytime I run my script it gets to Testing for differential expression and regulation in locus and then the program is killed. Each time I run it, the program gets to a different %. Below it shows 0%, last time it ran until 8%.
I am running cufflinks-2.2.1.Linux_x86_64 on linux mint 17.1 (64 bit).
I tried to look on the cuffdiff google groups and there is one account of others finding this error (https://groups.google.com/forum/#!searchin/tuxedo-tools-users/Testing$20for$20differential$20expression$20and$20regulation$20in$20locus.$20killed/tuxedo-tools-users/6c8U6-eJ2sg/dAxdILHZGPkJ), however there is no response from the superusers. So I thought I would try here.
my script is
cuffdiff /Ppatens_251_v3.0.gene.gtf -b /ppatens3.fa -N -L "case","control" -o "./diff_quant" --multi-read-correct /caseabundances.cxb /controlabundances.cxb
and here is the edited output (it was a bit long to post)
You are using Cufflinks v2.2.1, which is the most recent release.
[08:57:47] Loading reference annotation and sequence.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[08:57:56] Inspecting maps and determining fragment length distributions.
[09:34:25] Modeling fragment count overdispersion.
> Map Properties:
------------------------------------------------------------------------------------
Map Properties:
> Normalized Map Mass: 2254070.93
> Raw Map Mass: 1700540.11
> Number of Multi-Reads: 81811 (with 210967 total hits)
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[10:33:47] Calculating preliminary abundance estimates
> Processed 24675 loci. [*************************] 100%
[16:14:35] Learning bias parameters.
[20:37:21] Testing for differential expression and regulation in locus.
> Processing Locus Chr01:672743-675436 [ ] 0%Killed
I am trying to run cuffdiff after running cuffmerge but everytime I run my script it gets to Testing for differential expression and regulation in locus and then the program is killed. Each time I run it, the program gets to a different %. Below it shows 0%, last time it ran until 8%.
I am running cufflinks-2.2.1.Linux_x86_64 on linux mint 17.1 (64 bit).
I tried to look on the cuffdiff google groups and there is one account of others finding this error (https://groups.google.com/forum/#!searchin/tuxedo-tools-users/Testing$20for$20differential$20expression$20and$20regulation$20in$20locus.$20killed/tuxedo-tools-users/6c8U6-eJ2sg/dAxdILHZGPkJ), however there is no response from the superusers. So I thought I would try here.
my script is
cuffdiff /Ppatens_251_v3.0.gene.gtf -b /ppatens3.fa -N -L "case","control" -o "./diff_quant" --multi-read-correct /caseabundances.cxb /controlabundances.cxb
and here is the edited output (it was a bit long to post)
You are using Cufflinks v2.2.1, which is the most recent release.
[08:57:47] Loading reference annotation and sequence.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[08:57:56] Inspecting maps and determining fragment length distributions.
[09:34:25] Modeling fragment count overdispersion.
> Map Properties:
------------------------------------------------------------------------------------
Map Properties:
> Normalized Map Mass: 2254070.93
> Raw Map Mass: 1700540.11
> Number of Multi-Reads: 81811 (with 210967 total hits)
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[10:33:47] Calculating preliminary abundance estimates
> Processed 24675 loci. [*************************] 100%
[16:14:35] Learning bias parameters.
[20:37:21] Testing for differential expression and regulation in locus.
> Processing Locus Chr01:672743-675436 [ ] 0%Killed
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