Question: CuffDiff error on Local Galaxy
0
gravatar for ChickenRNA
18 months ago by
ChickenRNA50
ChickenRNA50 wrote:

HI, I am running local instance of Galaxy on my linux mint system. When I try to run CuffDiff, I am getting the following error (see below) When I look in the folder "/home/vythegi/galaxy1111/database/jobs_directory/000/" I cannot find a folder named (150" or tool_script.sh. I would really appreciate it if you can help me sort this out. Thanks in advance for your time.

Fatal error: Exit code 127 () [09:23:24] Loading reference annotation. Warning: No conditions are replicated, switching to 'blind' dispersion method [09:23:25] Inspecting maps and determining fragment length distributions. [09:26:02] Modeling fragment count overdispersion. Map Properties: Normalized Map Mass: 6915184.62 Raw Map Mass: 6698481.22 Fragment Length Distribution: Empirical (learned) Estimated Mean: 179.51 Estimated Std Dev: 60.34 Map Properties: Normalized Map Mass: 6915184.62 Raw Map Mass: 7110254.01 Fragment Length Distribution: Empirical (learned) Estimated Mean: 186.65 Estimated Std Dev: 62.64 [09:26:51] Calculating preliminary abundance estimates [09:26:51] Testing for differential expression and regulation in locus. Processed 6432 loci.
Performed 5391 isoform-level transcription difference tests Performed 5209 tss-level transcription difference tests Performed 5148 gene-level transcription difference tests Performed 0 CDS-level transcription difference tests Performed 0 splicing tests Performed 0 promoter preference tests Performing 0 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 /home/vythegi/galaxy1111/database/jobs_directory/000/150/tool_script.sh: line 9: R: command not found"

rna-seq local cuffdiff • 481 views
ADD COMMENTlink written 18 months ago by ChickenRNA50
1

Presumably your cummerbund issue is causing this, since cuffdiff alone wouldn't call R. Try to repair that one and see if it fixes things.

BTW, the lack of the 150 directory is probably due to a setting in galaxy.ini (there's one related to "cleanup" that is probably set to always).

ADD REPLYlink written 18 months ago by Devon Ryan1.9k

Thanks Devon, I am not sure how to repair it. I tried uninstalling and reinstalling, but that doesn't seem to work. Any suggestions?

ADD REPLYlink written 18 months ago by ChickenRNA50

More specifically this is the error that I have for CummberRbund version 2.8.2 "* installing source package ‘bitops’ ... * package ‘bitops’ successfully unpacked and MD5 sums checked * libs In file included from bit-ops.c:1:0: /home/vythegi/galaxy1111/database/dependencies/R/3.1.2/iuc/package_r_3_1_2/4d2fd1413b56/lib/R/include/R.h:28:20: fatal error: stdlib.h: No such file or directory compilation terminated. make: * [bit-ops.o] Error 1 ERROR: compilation failed for package ‘bitops’ * removing ‘/home/vythegi/galaxy1111/database/dependencies/cummeRbund/2.8.2/iuc/package_cummerbund_2_8_2/754912f24120/bitops’"

Any suggestions on how to fix this would be greatly appreciated. Thanks

ADD REPLYlink written 18 months ago by ChickenRNA50

When I go look in my "manage installed tools" there are a few tools that says "installed, missing tool dependencies", and Cummerbund is one of them. When looking at the specific error for the cummerbund it says "This tool dependency's required tool dependency cummerRbund version 2.8.2 has a status error" not sure if this is related to the error I have been getting. Thanks

ADD REPLYlink written 18 months ago by ChickenRNA50
2
gravatar for Devon Ryan
18 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Please preprend 4 spaces to each line of error messages, that will keep them in their native formatting.

Anyway, it appears that you don't have the normal compilation headers on your system. I have no clue how that could happen, but presumably googling for "stdlib.h install" and your linux distribution will reveal what to install.

ADD COMMENTlink written 18 months ago by Devon Ryan1.9k
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