simple_consensus_caller , how to automatically remove

[jelber2]

Hi,

I am getting an error while trying to use the steps of the simple_consensus_caller that presumably suggests that the ccs reads and subreads are out of order, but they do not seem to be. I am guessing maybe that the error is actually occurring because there is only one subread for the ccs read?

python ~/git/VariantWorks/samples/simple_consensus_caller/pileup_hdf5_generator.py --draft-file ../9.ccs-all.bam --subreads-file 9.bam --reference /nfs/scistore16/itgrp/bioinf/projects/DA0030/2021_Aug_27/analysis.5/raw/pg_asm-0.4.10/Sample9/9-peregrine-2021-0.4.10-3x-circlator.fasta -o train.hdf -t 4
Working directory /tmp/variantworks_consensus_sample_pileup_hdf5_06.03.2022-12:42:28_l3big6u_...
Traceback (most recent call last):
  File "/nfs/scistore16/itgrp/jelbers/git/VariantWorks/samples/simple_consensus_caller/pileup_hdf5_generator.py", line 386, in <module>
    generate_hdf5(parsed_args)
  File "/nfs/scistore16/itgrp/jelbers/git/VariantWorks/samples/simple_consensus_caller/pileup_hdf5_generator.py", line 315, in generate_hdf5
    for out in pool.imap(encode_func, folders_to_encode):
  File "/nfs/scistore16/itgrp/jelbers/miniconda3/envs/variantworks/lib/python3.7/multiprocessing/pool.py", line 748, in next
    raise value
AssertionError: There is a mismatch in the entries order in the draft and draft2ref file: draft:4194672, draft2ref:4194781

samtools view ../9.bam |cut -f 1|grep -B 5 -A 5 '4194672'

m54067_210310_022505/4194647/2053_13288
m54067_210310_022505/4194647/13375_24834
m54067_210310_022505/4194647/24919_36135
m54067_210310_022505/4194647/36210_47943
m54067_210310_022505/4194647/48024_59324
m54067_210310_022505/4194672/11921_16354
m54067_210310_022505/4194781/0_474
m54067_210310_022505/4194781/550_5298
m54067_210310_022505/4194781/5377_10291
m54067_210310_022505/4194781/10369_15096
m54067_210310_022505/4194781/15174_19826

samtools view ../9.ccs-all.bam |cut -f 1|grep -B 5 -A 5 '4194672'
m54067_210310_022505/4194592/ccs
m54067_210310_022505/4194622/ccs
m54067_210310_022505/4194629/ccs
m54067_210310_022505/4194645/ccs
m54067_210310_022505/4194647/ccs
m54067_210310_022505/4194672/ccs
m54067_210310_022505/4194781/ccs
m54067_210310_022505/4194803/ccs
m54067_210310_022505/4194806/ccs
m54067_210310_022505/4194823/ccs
m54067_210310_022505/4194829/ccs