trouble running prepare

[mkostich]

I have tried GTFs from several sources, including Homo_sapiens.GRCh38.110.gtf https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz; also from NCBI, both mouse and human; but I keep getting this error:

pybedtools.helpers.BEDToolsError:
Command was:

   bedtools subtract -s -b /tmp/pybedtools.ltn85in9.tmp -a /tmp/pybedtools._7stsyty.tmp

Error message was:
Error: unable to open file or unable to determine types for file /tmp/pybedtools._7stsyty.tmp
Please ensure that your file is TAB delimited (e.g., cat -t FILE).
Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED).

Here is an example command:
/opt/SCAPE/main.py prepare --gtf chr1.sort.gtf --prefix chr1_sort

I checked and see no signs of anything but tab delimiters in the gtfs; spaces are only found in the last column; if I try to get rid of those spaces, other issues arise (e.g. UnboundLocalError: cannot access local variable 'gene_type_id' where it is not associated with a value)

BTW I do get a _utr.bed file, but have no idea if it is finalized.

Do you have any idea about this? Where is it trying to write temporary files? I can read/write /tmp but don't see the files mentioned. It would be nice if you included a small GTF in your example_data to help with debugging.

Thanks for any help you can provide!

Mitch

[shyaman]

Hello @zhou-ran,

Thank you for your intriguing work. I am currently encountering the same issue, as have others (#12 #5 #6 #2). Given that it appears to be a bug with bedtools, could you please upload and share the processed human and mouse GTF files with us? This would greatly facilitate our use of the tool. Once again, thank you.

Shyaman

[houruiyan]

Hi @zhou-ran ,

Thank you for your great work. I also have the similar issue. Could you help to check? Thank you!

Best regards,
Ruiyan

[houruiyan]

Hi , I solved this problem. The right version of bedtools is v2.26.0. When I changed my bedtools to v2.26.0, then I can run prepare smoothly.

[houruiyan]

(scape) [ruiyanhou@CPU3:SCAPE]$ bedtools sort -i /mnt/ruiyanhou/nfs_share2/annotation/annotation_from_cellranger/refdata-gex-GRCh38-2020-A/genes/genes.gtf | gzip > GRCh38_cr.gtf.gz

(scape) [ruiyanhou@CPU3:SCAPE]$ python /mnt/ruiyanhou/nfs_share2/software/SCAPE/main.py prepare --gtf GRCh38_cr.gtf.gz --prefix GRCh38

The above is my code. You should first do sorting by using bedtools to get the sorted files and then run SCAPE prepare