[Iplant-api-dev] status FINISHED vs. ARCHIVING_FINISHED, no data

[Khalfan, Mohammed]

Is this an issue with our wrapper script?

I just tried another job (id: 36121) and I got the same result (FINISHED, no data in output folder).

From: Rion Dooley [mailto:dooley at tacc.utexas.edu]
Sent: Wednesday, December 11, 2013 1:00 PM
To: Khalfan, Mohammed
Cc: iPlant API Developers Mailing List
Subject: Re: [Iplant-api-dev] status FINISHED vs. ARCHIVING_FINISHED, no data

Looking at the error log it seems like the wrapper script bombed out somewhere around line 276 during execution.

curl -sku "mkhalfan:******" https://foundation.iplantc.org/apps-v1/job/36113/output/mkhalfan-36113-1386776891000/cd389-36113.err
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
102  2669  102  2669    0     0   5368      0 --:--:-- --:--:-- --:--:-- 45237
Inspecting list of GTF files to merge...
Executing cuffmerge -p 16 -o cuffmerge_out -g annotation.gtf -s genome.fas gtf_to_merge.txt...

[Wed Dec 11 10:09:08 2013] Beginning transcriptome assembly merge
-------------------------------------------

[Wed Dec 11 10:09:08 2013] Preparing output location cuffmerge_out/
[Wed Dec 11 10:09:15 2013] Converting GTF files to SAM
[10:09:15] Loading reference annotation.
[10:09:16] Loading reference annotation.
[10:09:17] Loading reference annotation.
[10:09:19] Loading reference annotation.
[10:09:21] Loading reference annotation.
[10:09:22] Loading reference annotation.
[10:09:23] Loading reference annotation.
[10:09:25] Loading reference annotation.
[10:09:27] Loading reference annotation.
[Wed Dec 11 10:09:29 2013] Quantitating transcripts
You are using Cufflinks v2.1.1, which is the most recent release.
Command line:
cufflinks -o cuffmerge_out/ -F 0.05 -g annotation.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 16 cuffmerge_out/tmp/mergeSam_filemtqH90
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File cuffmerge_out/tmp/mergeSam_filemtqH90 doesn't appear to be a valid BAM file, trying SAM...
[10:09:29] Loading reference annotation.
[10:09:33] Inspecting reads and determining fragment length distribution.
Processed 98978 loci.
> Map Properties:
> Normalized Map Mass: 358518.00
> Raw Map Mass: 358518.00
> Fragment Length Distribution: Truncated Gaussian (default)
>               Default Mean: 200
>           Default Std Dev: 80
[10:09:35] Assembling transcripts and estimating abundances.
Processed 98978 loci.
[Wed Dec 11 10:10:16 2013] Comparing against reference file annotation.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
No fasta index found for genome.fas. Rebuilding, please wait..
Fasta index rebuilt.
[Wed Dec 11 10:11:22 2013] Comparing against reference file annotation.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
DONE!
  total 295M
drwx------ 3 iplant G-802086 4.0K Dec 11 10:12 .
drwxrwxr-x 7 iplant G-802086 4.0K Dec 11 10:12 ..
drwx------ 2 iplant G-802086 4.0K Dec 11 10:09 logs
-rw------- 1 iplant G-802086 148M Dec 11 10:12 merged.gtf
-rw------- 1 iplant G-802086 150M Dec 11 10:12 merged_with_ref_ids.gtf


/tmp/slurmd/job2214500/slurm_script: line 276: syntax error near unexpected token `;'
/tmp/slurmd/job2214500/slurm_script: line 276: `if ! [[ -s $SAM_1F ]]; then;'

--
Rion



On Dec 11, 2013, at 10:33 AM, Khalfan, Mohammed <mkhalfan at cshl.edu<mailto:mkhalfan at cshl.edu>> wrote:


Hi,

One of my jobs, 36113, seems to have completed with status "FINISHED". There is no data in the specified archive path. I have seen this before. Can you tell me why this is happening/help me get this working properly?

Thank you,
Mohammed



Mohammed Khalfan
Bioinformatics Developer
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor NY 11724
(516)367-5162
www.dnalc.org<http://www.dnalc.org/>

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