Question: htseq-count crashed again and again
0
gravatar for andrewzlobin
4 weeks ago by
andrewzlobin10
andrewzlobin10 wrote:

htseq-count crashed again and again Usegalaxy.org)

Running output file from HiSat2, Runs for 20 min and give message:
error
An error occurred with this dataset:
Fatal error: Unknown error occured
[bam_sort_core] merging from 62 files and 1 in-memory blocks...
100000 GFF lines processed.
200000 GFF lines processed.
300000 GFF lines processed.
400000 GFF lines processed.
500000 GFF lines processed.
600000 GFF line

Whats wrong? Space is OK -50% z

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by andrewzlobin10
0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There are a few problems:

  • This tool does not accept data in GFF3 format. It does accept GTF format and GFF format that includes key attributes of strict GTF format.
  • The reference annotation in now an error state due to the failed conversion to other datatypes.
  • The reference annotation is based on the Ensembl genome build/version, which has chromosome naming mismatch problems versus the UCSC rn6 genome build/version used for mapping.

Choices:

  • All inputs must be based on the same genome build/version for errors or unexpected results can occur.
  • Find a GTF version of the annotation based on rn6. Many data sources will provide both. For UCSC's rn6 genome build/version, iGenomes is one provider for reference annotation. Download the tar archive locally, uncompress, and Upload just the genes.gtf dataset to Galaxy. https://support.illumina.com/sequencing/sequencing_software/igenome.html
  • The tool gffread can convert GFF3 to GFT, but the original GFF3 still needs to be based on the same genome build/version. The one you have currently will not work.

All of the above is covered in the Support FAQs: https://galaxyproject.org/support/#troubleshooting

Galaxy tutorials, including those for RNA-seq: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for andrewzlobin
4 weeks ago by
andrewzlobin10
andrewzlobin10 wrote:

i am very grateful, thanks a lot. I am doing what you recommend. Just another question, for HISAT I was using the fast file. Is it supposed to be also from UCSC? I don't remember where I downloaded it.

Thanks Andrei

ADD COMMENTlink written 4 weeks ago by andrewzlobin10

Cross-posted here: https://biostar.usegalaxy.org/p/28491/

ADD REPLYlink written 4 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for andrewzlobin
4 weeks ago by
andrewzlobin10
andrewzlobin10 wrote:

Dear Jennifer, I uploaded Rattus_norvegicus_UCSC_rn6.tar, Htseq-count still doesn't work. ???

Feature-count does work!!! with this dataset!!!! Fantastic! I hope this will sort out problem.

Thanks a lot Andrew

ADD COMMENTlink written 4 weeks ago by andrewzlobin10
0
gravatar for andrewzlobin
4 weeks ago by
andrewzlobin10
andrewzlobin10 wrote:

Great I was able to run featurecounts output files on DeSeq2. All work.fantastic Thanks a lot.

ADD COMMENTlink written 4 weeks ago by andrewzlobin10
0
gravatar for andrewzlobin
4 weeks ago by
andrewzlobin10
andrewzlobin10 wrote:

With the most resent rat annotation file I was able to run HTseq-count on my data. But after that when I try to run output files on DESeq2 it crashes:" Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in row.names<-.data.frame(*tmp*, value = value) : duplicate 'row.names' are not

What's the reasons? Thanks Andrew

ADD COMMENTlink written 4 weeks ago by andrewzlobin10
0
gravatar for andrewzlobin
4 weeks ago by
andrewzlobin10
andrewzlobin10 wrote:

Sorry I found the problem. Thanks Andrew

ADD COMMENTlink written 4 weeks ago by andrewzlobin10
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