warning [E::idx_find_and_load] Could not retrieve index file for

[CCCKW]

pairtools parse /cluster/home/Kangwen/Hic/data_new/snHic_index/XY5/snHic_SRR0_tmp/SRR0.qc.bam -c /cluster/home/Kangwen/common/hg38/hg38.fa.chrom.sizes --drop-sam --drop-seq --output-stats SRR0.stats --assembly hg38 --no-flip --add-columns mapq --walks-policy all -o SRR0.pairs.gz --nproc-in 60 --nproc-out 60
[E::idx_find_and_load] Could not retrieve index file for '/cluster/home/Kangwen/Hic/data_new/snHic_index/XY5/snHic_SRR0_tmp/SRR0.qc.bam'
writer fwrite: bug encountered
writer writer_write_block: bug encountered

How to solve this?

[golobor]

A quick question - the error message suggests that it's missing an index file - have you tried indexing the .bam file?

[Phlya]

A quick question - the error message suggests that it's missing an index file - have you tried indexing the .bam file?

To index a bam file it needs to be sorted, which breaks pairtools.

[CCCKW]

A quick question - the error message suggests that it's missing an index file - have you tried indexing the .bam file?

To index a bam file it needs to be sorted, which breaks pairtools.

how to index the .bam file?

[Phlya]

I don't know why you might be getting this error, pairtools doesn't need an index generally...

I think that is just a warning that I have been seeing recently also, and the error is actually something else, about writing? Maybe you don't have permissions to write in the folder, or no space?.. Not sure.

[Phlya]

pysam-developers/pysam#939

[CCCKW]

After running pairtools parse, the column of pairtype in the .pairs files I got was 'XX'. Whether this is the reason?

[Phlya]

The pairs you are showing are all unmapped (! for both chromosomes), so the pair type XX is normal for them.

[amvarani]

I have a similar warning here, but pairtools parse continues and generates the pairsam file.

[E::idx_find_and_load] Could not retrieve index file for 'aligned.bam'

[Phlya]

Yes, the warning by itself is harmless.