Question: Error message when processing htseq-count
gravatar for jramo033
7 days ago by
jramo03320 wrote:

When running htseq count, I got this error message:

Fatal error: Unknown error occured [bam_sort_core] merging from 9 files and 1 in-memory blocks... Error occured when processing GFF file (line 2 of file /galaxy-repl/main/files/026/998/dataset_26998011.dat): Strand must be'+', '-', or '.'.

These are the first lines of my GFF fille and I do not see the error:

#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinID alignID 
uc001aaa.3 chr1 + 11873 14409 11873 11873 3 11873,12612,13220, 12227,12721,14409,  uc001aaa.3 
uc010nxr.1 chr1 + 11873 14409 11873 11873 3 11873,12645,13220, 12227,12697,14409,  uc010nxr.1 
uc010nxq.1 chr1 + 11873 14409 12189 13639 3 11873,12594,13402, 12227,12721,14409, B7ZGX9 uc010nxq.1
gff gft galaxy gff3 htseq • 47 views
ADD COMMENTlink modified 7 days ago • written 7 days ago by jramo03320
gravatar for Jennifer Hillman Jackson
7 days ago by
United States
Jennifer Hillman Jackson25k wrote:


The file appears to be in BED12 format, not GFF/GTF.

Use GTF format or a hybrid GFF-GTF format for this input. Avoid GFF3 format, HT-seq count only accepts the other two. Header "#" lines are also problematic and should be removed when you do find an annotation source.

Gencode and iGenomes both have human reference annotation that is a match for UCSC-sourced reference genomes. The UCSC Table browser will output GTF format for tracks, but the transcript_id and gene_id values will be the same (both will be the "transcript_id"). This is usually an undesirable scientific content issue, as all counts will be "by transcript", even if processed/labeled as being "by gene". Try one of the other sources instead.


Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 days ago by Jennifer Hillman Jackson25k
gravatar for jramo033
7 days ago by
jramo03320 wrote:

Jen, thank you for your prompt response. How do I import directly to Galaxy from Gencode and iGenomes ( I used "Get data" to import from UCSC but I don't see options for Gencode and iGenomes )

ADD COMMENTlink written 7 days ago by jramo03320

These data do not have a distinct "Get Data" tool.

For Gencode, copy the link to the GTF and paste it into the Upload tool. Hg38 data is here (with a link to hg19, if mapping with that genome build/version instead):

For iGenomes, the archive corresponding to the target genome/build needs to be locally downloaded, the tar archive unpacked, and then just the genes.gtf data uploaded to Galaxy (browse the local file, or use FTP). Find all available genome/builds here:

Upload FAQs: >> Loading Data

Hope that helps!

ADD REPLYlink written 7 days ago by Jennifer Hillman Jackson25k
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