genomematt / xenomapper2 Goto Github PK

Multiple issues with docopt with no clear method to resolve
Will revert to using argparse

Master has been renamed main

Do BAM reading and decompression in at least one thread per BAM. Consider threads for output files.

When running xenomapper2 on bams mapped by bwa mem I get the following errors from pylazybam:

xenomapper2 v2.0rc1 --primary=/scratch-shared/fmlab/nmoldovan/tmp/FM_seq_020/trimmed/7_xenomapper/1_mapping/LP0051_08_L001_primary.bam --secondary=/scratch-shared/fmlab/nmoldovan/tmp/FM_seq_020/trimmed/7_xenoma$

Traceback (most recent call last):
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/bin/xenomapper2", line 8, in
sys.exit(main())
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/cli.py", line 193, in main
pair_counts, counts, writer = xenomap(primary_bam,
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/xenomapper2.py", line 884, in xenomap
forward_state, reverse_state = xenomap_states(primary_aligns,
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/xenomapper2.py", line 685, in xenomap_states
prim_f_AS, prim_f_XS = score_function(prim_f_aligns,
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/xenomapper2.py", line 314, in get_bamprimary_AS_XS
AS = AS_function(bamprimary[0])
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/pylazybam/tags.py", line 55, in get_AS
raise ValueError(
ValueError: More than one match to b'ASC.' was found in b'I\x01\x00\x00\x04\x00\x00\x00ASC\x01'<V\x17\x01\x00S\x00\x97\x00\x00\x00\x04\x00\x00\x00!SC\x01I\xff\xff\xffA01685:16:HGHWVDSX3:1:1258:25373:19100\x00p$

or

xenomapper2 v2.0rc1 --primary=/scratch-shared/fmlab/nmoldovan/tmp/FM_seq_020/trimmed/7_xenomapper/1_mapping/LP0051_07_L001_primary.bam --secondary=/scratch-shared/fmlab/nmoldovan/tmp/FM_seq_020/trimmed/7_xenoma$

Traceback (most recent call last):
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/bin/xenomapper2", line 8, in
sys.exit(main())
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/cli.py", line 193, in main
pair_counts, counts, writer = xenomap(primary_bam,
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/xenomapper2.py", line 884, in xenomap
forward_state, reverse_state = xenomap_states(primary_aligns,
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/xenomapper2.py", line 685, in xenomap_states
prim_f_AS, prim_f_XS = score_function(prim_f_aligns,
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/xenomapper2/xenomapper2.py", line 315, in get_bamprimary_AS_XS
XS = XS_function(bamprimary[0])
File "/gpfs/home1/norbertm/projects/code/core_pipeline_310322/workflow/rules/7_xenomapper/.snakemake/conda/39b62994/lib/python3.10/site-packages/pylazybam/tags.py", line 108, in get_XS
raise ValueError(
ValueError: More than one match to b'XSC.' was found in b'N\x01\x00\x00\x07\x00\x00\x00XSC\x02'<V\x1b\x01\x00S\x00\x97\x00\x00\x00\x07\x00\x00\x00QSC\x02b\xff\xff\xffA01685:16:HGHWVDSX3:1:1161:21965:27946\x00p$

I am mapping and sorting reads in the previous step by:

bwa mem {params.ref} {input}
-M
-t {threads}
2> {log} |
samtools sort
-n
-@ {threads}
-o {output} 2>> {log}

Intriguingly this pipeline worked with another batch of files already, but now it is throwing the above error.

Edit: I forgot to add, that we are talking about 150 bp PE seq of genomic data.