Open EsperanzaDai opened 4 years ago
I have the same error, using the full snapATAC pipeline from fastq. Is the alignment stage supposed to create an index?
Side note: my run is not creating a snap file... I presumed this was the problem as it is the only error message I recieved
I also got the same error, following the snapATAC tutorial from fastq files. Could you please suggest how to solve the problem? Thank you.
Best regards.
I also used the Cell Ranger possorted_bam.bam file to generate a .snap.nsrt.bam file, but when I used the snaptools snap-pre function, I got:
[E::idx_find_and_load] Could not retrieve index file for 'path/filename.snap.nsrt.bam'
How should I resolve this issue? Thanks.
Hi all,
Since noone is responding to us, thought I would share my fix. Unfortunately my fix is that there is no fix. It appears as though this error is just a warning and that the correct indexes are generated or not required. In my case I was receiving an empty file after receiving this error because my computing system was running out of memory (unrelated to the error itself).
My scripts for submission of snaptools to a slurm based cluster system are here
Hopefully they can provide some help to get this working.
Dear Miss,
I have the same problem as you, I tried several solutions, and finally found it was the software version. I changed to SnapTools 1.4.8 and no more errors were reported
Dear Dr. Fang,
Thanks a lot for the tool!
I am trying to create the snap file from the Cell Ranger possorted_bam.bam files.
I followed the instructions: https://github.com/r3fang/SnapATAC/wiki/FAQs#cellranger_output But from the snap.nsrt.bam file, when I tried to create the snap file with the
snaptools snap-pre
, I got verbose during this step:[E::idx_find_and_load] Could not retrieve index file for 'myfilename.snap.nsrt.bam' However, I still got the snap files and they seem fine. I am wondering if this would be a problem though?
I also tried to index the 'myfilename.snap.nsrt.bam', but since it is sorted by name with $ samtools sort -n -@ 10 -m 1G myfilename_possorted.snap.bam -o myfilename.snap.nsrt.bam So, the index file could not be created.
Hope that you could help here.
Thanks a lot! Best,