[E::idx_find_and_load] Could not retrieve index file

[EsperanzaDai]

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,

[elliefewings]

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

[shhxiao19]

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.

[strawberry789]

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.

[elliefewings]

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.

[xiangzd]

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