mSINGs - pipeline

Question

[esimonova.me]

I am trying to run mSINGs and I am getting no success with that. All tests were pased after the installation.

scripts/run_msings.sh /soreted_bam/bam_list.txt ../hg19_set_satellites.bed ../../reference.list_baseline_21-03 ~/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa

This code returns the following error:

[mpileup] 1 samples in 1 input files
Traceback (most recent call last):
  File "/home/xxx/MSI/msings/msings-env/bin/msi", line 4, in <module>
    __import__('pkg_resources').run_script('msings===0229.7510b3f', 'msi')
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 667, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1464, in run_script
    exec(code, namespace, namespace)
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/msings-0229.7510b3f-py3.8.egg/EGG-INFO/scripts/msi", line 7, in <module>
    sys.exit(main(sys.argv[1:]))
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/msings-0229.7510b3f-py3.8.egg/msings/scripts/script.py", line 16, in main
    return action(arguments)
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/msings-0229.7510b3f-py3.8.egg/msings/subcommands/count_msi_samples.py", line 65, in action
    specimens, prefixes, fieldnames, variant_keys=eval(chosen_parser)
  File "<string>", line 1, in <module>
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/msings-0229.7510b3f-py3.8.egg/msings/parsers.py", line 26, in parse_msi
    control_info=natsort.natsorted(control_info, key=itemgetter('Position'))
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/natsort/natsort.py", line 259, in natsorted
    return sorted(seq, reverse=reverse, key=key)
  File "/home/xxx/MSI/msings/msings-env/lib/python3.8/site-packages/natsort/utils.py", line 209, in natsort_key
    val = key(val)
KeyError: 'Position'

MSI.bed has the following structure:

chr2    47641559        47641560        BAT26
chr2    95849361        95849362        NR-24
chr4    55598211        55598212        BAT25
chr11   125490765       125490766       NR-27
chr14   23652346        23652346        NR-21

The reference baseline file looks the following:

> chromosome      location        repeat_unit_length     
> repeat_unit_binary      repeat_times    left_flank_binary  
> right_flank_binary      repeat_unit_bases       left_flank_bases      
> right_flank_bases       threshold   supportSamples chr2    47641559   
> 1       0       27      299     687     A       CAGGT   GGGTT  
> 0.262192        21 chr2    95849361        1       3       23      860     738     T       TCCTA   GTGAG   0.130544        23 chr4    55598211   
> 1       3       25      1016    544     T       TTTGA   GAGAA  
> 0.143718        23 chr11   125490765       1       3       21      520     51      T       GAAGA   AATAT   0.074239        23 chr14   23652346   
> 1       0       21      999     660     A       TTGCT   GGCCA  
> 0.072881        23