Question: htseq-count crashed again and again
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 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 5 months ago • written 5 months ago by andrewzlobin20
0
gravatar for Jennifer Hillman Jackson
5 months 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 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 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 5 months ago by andrewzlobin20

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

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 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 5 months ago by andrewzlobin20
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 wrote:

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

ADD COMMENTlink written 5 months ago by andrewzlobin20
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 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 5 months ago by andrewzlobin20
0
gravatar for andrewzlobin
5 months ago by
andrewzlobin20
andrewzlobin20 wrote:

Sorry I found the problem. Thanks Andrew

ADD COMMENTlink written 5 months ago by andrewzlobin20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 182 users visited in the last hour