At the beginning of the process I get this warning:
Warning: Read HS1_07961:1:1308:18104:63516#3 claims to have an aligned mate which could not be found in an adjacent line.
Then, at the end of the SAM file, I get:
10800000 SAM alignment record pairs processed.
10900000 SAM alignment record pairs processed.
Error occured when processing SAM input (record #11138334 in file 7961_1_3.bam):
reference_id -1 out of range 0<=tid<22
[Exception type: ValueError, raised in calignmentfile.pyx:640]
and my output .count file was empty, with 0 byte.
The code I entered for this process is: htseq-count -f bam -s no -a 10 7961_1_3.bam Mus_musculus.GRCm38.82.gtf > 7961_1_3.count
note that my BAM files contain pair ended strands.
Any help will be appreciated!
Thank you in advance.