Blobtools add --cov error.

[COCOJJLEE]

Environment:
Centos7
Python = 3.9.13
blobtoolkit = 4.1.4

Input data processing:
pacbio hifi read
minimap2 -ax asm20 ${organism}.asm.p_ctg.fa ${organism}.cutadapt.output.fastq > ${organism}.sam
samtools view -Sb ${organism}.sam > ${organism}.bam
samtools sort ${organism}.bam > ${organism}.sort.bam
samtools index ${organism}.sort.bam

Error command:
blobtools add --cov ${organism}.sort.bam BlobDir/

Error message:
Traceback (most recent call last):
File "/home/.conda/envs/blobtools/bin/blobtools", line 8, in
sys.exit(cli())
File "/home/.conda/envs/blobtools/lib/python3.9/site-packages/blobtools/blobtools.py", line 105, in cli
sys.exit(subcommand())
File "/home/.conda/envs/blobtools/lib/python3.9/site-packages/blobtools/lib/add.py", line 203, in cli
main(args)
File "/home/.conda/envs/blobtools/lib/python3.9/site-packages/blobtools/lib/add.py", line 149, in main
parsed = field["module"].parse(
File "/home/.conda/envs/blobtools/lib/python3.9/site-packages/blobtools/lib/cov.py", line 182, in parse
fields = parse_bam(
File "/home/.conda/envs/blobtools/lib/python3.9/site-packages/blobtools/lib/cov.py", line 43, in parse_bam
os.remove(index_file)
FileNotFoundError: [Errno 2] No such file or directory: 'Elophila_nymphaeata.sort.bam.csi'

When I ran that task 3 months ago, it worked fine, but I recently encountered the issue.
Is there any way to fix this?
blobtools add --busco and blobtools create --fasta work well

Sincerely

[tanpham15]

Hi, I got the similar error, and it looks like no index file, .csi in your directory

I think you might need to index the bam file again (samtools index -c name.sort.bam). Note: also you should remove the bam.bai before blobtools add --busco. When I have both .bai and .csi, the error occurred.

Good luck.