I am able to import GTEx BAM files (and indexes) into my Galaxy instance.
But when I try to use htseq_counts (to get transcript counts from the alignment) I get this error message:
[E::hts_hopen] Failed to open file /galaxy/server/database/objects/0/7/6/dataset_076d96d0-7fbd-4b1b-a57d-809a4c95e0ee.dat
[E::hts_open_format] Failed to open file /galaxy/server/database/objects/0/7/6/dataset_076d96d0-7fbd-4b1b-a57d-809a4c95e0ee.dat
samt
And when doing a simple samtools idxstats returns this error:
(upload://dmMSwup0syhcNRAW2SU3u8SYQiA.png)
( /galaxy/server/database/jobs_directory/000/5/tool_script.sh: line 22: /galaxy/server/database/objects/e/3/f/dataset_e3fcc04d-4646-4de3-8ce4-955206f0b2df.dat: No such file or directory )
I tested this on at least two different alignments.
Is this an issue with how it is loaded into Galaxy, or an issue with the BAM files?
The issue with htseq_counts seems to be resolved. It was recognizing the index file, instead of the actual BAM files.
However, I am not sure why samtools idxstats command will not work. I receive the same error message.
From Terra Support 9:23am EST
Your request (114080) has been received and is being reviewed by our support staff.
From Terra Support 9:38am
Is the main issue with the
samtools idxstatscommand on uploaded files? Resulting in this error?