search

PacificBiosciences / pb-CpG-tools

Collection of tools for the analysis of CpG data
BSD 3-Clause Clear License
74 stars 6 forks source link

file has no sequences defined (mode='rb') - is it SAM/BAM format? #6

Closed jdakota1305 closed 2 years ago

jdakota1305 commented 2 years ago

Hi All,

Excited to use this, but am running into issues when supplying an output from primrose to the CpG tool. I had no issue generating the bam file and index from primrose, but it doesn't seem to be working when I pass it to the the CpG tool. I have attached the log as well. Thanks in advance!

m5c.output-aligned_bam_to_cpg_scores.log

Chunking regions for multiprocessing. Traceback (most recent call last): File "/fh/fast/johnston_c/bamsieve/jd-m4c/a95dc47b-b631-46e8-4dcb-e15857563cf3/aligned_bam_to_cpg_scores.py", line 981, in main() File "/fh/fast/johnston_c/bamsieve/jd-m4c/a95dc47b-b631-46e8-4dcb-e15857563cf3/aligned_bam_to_cpg_scores.py", line 966, in main regions_to_process = get_regions_to_process(args.bam, args.fasta, args.chunksize, args.modsites, File "/fh/fast/johnston_c/bamsieve/jd-m4c/a95dc47b-b631-46e8-4dcb-e15857563cf3/aligned_bam_to_cpg_scores.py", line 138, in get_regions_to_process bamIn = pysam.AlignmentFile(input_bam, 'rb') File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 1000, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

rhallPB commented 2 years ago

The pileup tool requires an aligned bam, it does not carry out the actual alignment. The results from primrose should be aligned to the reference with pbmm2 before calculation of the pileup.