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Question: Unknown error on HTseq_count
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gravatar for wei.wang
10 months ago by
wei.wang • 0
wei.wang • 0 wrote:

Hi, I’m trying to do RNA_seq analysis with Galaxy. I upload the hg38 iGenome from illumina to my history, but when I run HTseq_count on my HISAT output file, there was always a error messag:

Fatal error: Unknown error occurred 100000 GFF lines processed.
200000 GFF lines processed.
300000 GFF lines processed.
400000 GFF lines processed.
500000 GFF lines processed.
600000 GFF lines processed.
700000 GFF lines processed.
800000 GFF lines processed.
900000 GFF lines processed.
1000000 GFF lines processed.
Error occured when processing GFF file (line 1065950 of file /galaxy-repl/main/files/023/332/dataset_23332282.dat) : need more than 3 values to unpack
[Exception type: ValueError, raised in __init__.py:207]

I don’t know if the gtf file of iGenome is corrupted or something wrong with my data?
ftp upload gtf dataset htseq_count • 352 views
ADD COMMENT • link •
modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by wei.wang • 0
0
gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like errors that come up when a dataset is not completely uploaded (truncated). Check the end of the iGenomes genes.gtf file to see if it is complete. Use the tool Select last lines from a dataset. Other data problems are possible but start there.

If truncated, first double check that your local version of the file is complete, then reload to Galaxy with FTP.

If not truncated, please let us know and we can troubleshoot more.

FAQs:

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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