HISAT2 output error

Question: HISAT2 output error

6 months ago by

carrollc2 • 0 wrote:

Hello,

We recently ran a set of samples through galaxy from Genewiz. Of our samples, two are not working. Following upload onto Galaxy, we ran these files using HISAT2 version 2.0.5.2 as we did all of our other files. The other files output correctly and were able to be run through htseq and DESeq. However, the output for our problem files following completion of the HISAT is: gzip: input_r.fastq.gz: not in gzip format Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): hisat2-align died with signal 6 (ABRT) (core dumped)

I've tried using the most recent version, re-uploading the files as fastqsanger files, and still receive no output for these files. Genewiz recently sent us their versions of the files which they analyzed and found no problems. Upon uploading these into Galaxy, we encountered the same error. Is there something we can do to resolve this file?

Thank you!

rna-seq hisat2 • 289 views

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modified 6 months ago • written 6 months ago by carrollc2 • 0

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I wasn't able to find the error HISAT2 job at Galaxy Main https://usegalaxy.org in your account. I do see other related work/successful runs.

If you are working at Galaxy Main and or can reproduce the problem there, a bug report can be sent in. Please leave the input and error datasets undeleted and include a link to this post in the comments so we can link the two.

You also might try loading the data using "autodetect" for the datatype in the Upload tool. This will uncompress the data and assign fastqsanger if the data meets specification. I would then suggest running FastQC on these and any other uploaded fastq data. Many format problems can be detected when that tool errors. Partially loaded data might be the problem - check the end of the file with the tool: Select last lines from a dataset (tail).

Troubleshooting FAQs: https://galaxyproject.org/support/#troubleshooting

My job ended with an error. What can I do? https://galaxyproject.org/support/tool-error/
And the first few FAQs in this section: https://galaxyproject.org/support/#getting-inputs-right

All that said, Galaxy Main has the pre-release for 18.05 currently on the server and a few problems have come up. Bug reports for errors are encouraged. Some are related to the Upload tool, as in this example (a small issue, the data is still usable): https://github.com/galaxyproject/usegalaxy-playbook/issues/115

Thanks! Jen, Galaxy team

ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

6 months ago by

carrollc2 • 0

carrollc2 • 0 wrote:

Hi Jennifer!

Thank you for the advice. In my Main in History "KB1A Part 3", they are listed as 23 and 22. They appear to be run as complete, but the information in the file returns that error code.

I will try the fastqsanger option and see if it works out!

Thanks!

ADD COMMENT • link written 6 months ago by carrollc2 • 0

Hi - I ran both FastQC and FastqGroomer on datasets 22 + 23 and both reported that the input is not in gzip compressed fastq format. I would definitely suggest uncompressing the data locally and taking a look at it. FastQC reported that a sequence identifier did not start with an "@" within the error (run the tool, then click on the bug report icon to view, but you don't need to submit it). There is some format problem with the fastq data (it may not be fastq) - so this is likely not just a gzip compression incompatibility.

Once the file is corrected, then try uploading using "autodetect" for the datatype. Then run FastQC to see what happens (it is a good idea to do this anyway). You might need to go back to your data provider if the problem is internal to the file (and not just a truncated data transfer at some point).

An example of fastq formatting is here: https://en.wikipedia.org/wiki/FASTQ_format

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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