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warning [E::idx_find_and_load] Could not retrieve index file for
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?
A quick question - the error message suggests that it's missing an index file - have you tried indexing the .bam file?
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.
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?
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.
After running pairtools parse, the column of pairtype in the .pairs files I got was 'XX'. Whether this is the reason?
The pairs you are showing are all unmapped (! for both chromosomes), so the pair type XX is normal for them.
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'
