collapse_isoforms_by_sam.py - can not iterate over samfile without header

[ckitsoulis]

Hello,

This the first time I am using Cupcake to handle IsoSeq data. I am trying to collapse HQ isoforms from IsoSeq reads (FASTA file) with collapse_isoforms_by_sam.py but it fails. I have already tried mapping the reads with minimap2 and GMAP in case the problem was caused by these tools and their produced SAM file, but the result is the same. I'm getting the following error:

'''
Traceback (most recent call last):
File "/home1/christos_k/software/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 452, in
main(args)
File "/home1/christos_k/software/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 330, in main
region_list_ignore, chunk_regions_list = multiprocess_predefine_regions(args.sam, args.cpus)
File "/home1/christos_k/software/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py", line 169, in multiprocess_predefine_regions
for prev in reader:
File "pysam/libcalignmentfile.pyx", line 1850, in pysam.libcalignmentfile.AlignmentFile.iter
NotImplementedError: can not iterate over samfile without header
'''

It would be very helpful if you could help me with this problem. Thank you.

Christos

[JBreunig]

FYI, I just ran into the same thing only when I tried to use multiple cpus (--cpus). It ran fine with the default 1.

[ckitsoulis]

FYI, I just ran into the same thing only when I tried to use multiple cpus (--cpus). It ran fine with the default 1.

Thank you for your response, I will give it a try. However, it seems to work fine with multiple CPUs and BAM file as input.