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Question: FastQC IndexError: list index out of range
0
gravatar for madkisson
3.6 years ago by
madkisson • 30
United States
madkisson • 30 wrote:

Hi

Yesterday the four runs that was doing failed at the FastQC stage - some were FastQC of fastqsanger files and some were of BAM files that had just been made by TopHat2. I can't really tell from teh reports whether or not this is an issue with my files or something on teh Galaxy end [this workflow as worked several times before without any such error]. Here is the error report:

Fatal error: Exit code 1 ()
Failed to process file XX_BAM.bam
java.lang.ArrayIndexOutOfBoundsException: -1
	at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.calculateDistribution(SequenceLengthDistribution.java:105)
	at uk.ac.babraham.FastQC.Modules.SequenceLengthDistribution.raisesError(SequenceLengthDistribution.java:189)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:334)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:163)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
	at java.lang.Thread.run(Thread.java:701)
Traceback (most recent call last):
  File "/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 162, in <module>
    fastqc_runner.run_fastqc()
  File "/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 136, in run_fastqc
    self.copy_output_file_to_dataset()
  File "/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/8c650f7f76e9/fastqc/rgFastQC.py", line 109, in copy_output_file_to_dataset
    with open(result_file[0], 'rb') as fsrc:
IndexError: list index out of range

Thanks
rnaseq fastqc cloudman • 2.0k views
ADD COMMENT • link •
modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by madkisson • 30
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is on your cloud instance, correct? Is this the first time you have run the tool on this server? There could be a tool install issue - uninstalling then reinstalling (with managed dependencies) could help.

That said, this type of error is generally associated with a problem with the format of the inputs. Meaning, the datasets do not align with the requirements of the tool. Troubleshooting help for format and similar issues is in the Galaxy wiki:
http://wiki.galaxyproject.org/Support Section 2.8

This error can also indicate that the memory required by the jobs exceeds the available resources on the server/nodes in use. Scaling up would be the solution in this case. Since this occurred on both fastq and bam datasets, this seems the most likely issue.

If you cannot resolve the issue, try to duplicate it on the public Main Galaxy server, and if it errors, send in a bug report and we can help more.

Thanks, Jen, Galaxy team


 
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen! I suspect it is in fact a memory issue, since I'm having a lot of those. The disk says it is at 99% [788G/800G] despite the fact that I've dumped a huge a mount of data and calculate that I'm actually at 195G/800G. When I attempt to increase the limit from 800G to 1000G, it just does nothing. This has been the case since yesterday and over at least 2 reboots

ADD REPLY • link written 3.6 years ago by madkisson • 30

 Never mind. I figured it out. 

ADD REPLY • link written 3.6 years ago by madkisson • 30

Glad it worked out. I believe you also sent in a bug report about this same issue - is that true and is it also resolved or do you need feedback? Thanks, Jen

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Yes the bug report was for the same memory issue. I was able to discover the list of histories I thought I'd deleted but had not 'permanently' deleted.

The original FastQC error issue, however, turns out NOT to be related to the memory problem. I ran the tool again and the error persists. I'm going to run the entire workflow again on this data and see if the same thing happens. Will report afterwards. Thanks

ADD REPLY • link written 3.6 years ago by madkisson • 30

Strange about the FastQC tool errors. After confirming the format of the inputs (this is the most common trigger for this error, on systems with enough resource and correct data dir & database config), perhaps double check that the install was complete? This was sourced from the Main Tool Shed, correct? Uninstalling (fully) and then installing again is one thing to try. This is the first report of a problem like this that I am aware of - but that doesn't mean that there couldn't be an issue necessarily. Another thing to try is to see if the issue can be replicated on Main. If so, send in the error as a bug report and we'll review the inputs and provide feedback. I know some of this is repeat info, but I wasn't sure how much of this you tried already. Feedback after a re-run, with these suggestions in mind, is welcomed - we want to help you get this going. Best, Jen

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

I retract my earlier dismissal of the memory issue being the culprit - I think the problem was the low memory screwing with my pipeline, just further up my pipeline, maybe the BAM files. Anyway, I've restarted everything and it's all working great. Thank you

ADD REPLY • link written 3.6 years ago by madkisson • 30
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