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ValueError: not enough values to unpack (expected 12, got 11) #32

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LucaBertoli opened this issue Jun 7, 2023 · 0 comments
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@LucaBertoli
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Hi,

I am trying to call SV on TellSeq human WGS ranging from 45X to 85X coverage. The analysis was performed with TellSort pipeline obtaining a phased BAM with the BX tag (not the HP tag).
In the past I already used LinkedSV to call variants on TellSeq data, and it worked fine. Now even if I use the same command line as the other samples:
/home/lucab/LinkedSV/linkedsv.py -i <<Full path to sample directory>>/T502.phased.bam -d <<full path to output directory>> -r /home/db/tellSeq_genome/hg38_UST/hg38_chrs.fasta -v hg38 -t 20 --wgs --somatic_mode --save_temp_files
I allways get the following error:

[06/05/2023 09:21:59 (171.954 MB)] searching for extremely high coverage region
Traceback (most recent call last):
  File "/home/lucab/LinkedSV/linkedsv.py", line 313, in <module>
    main()
  File "/home/lucab/LinkedSV/linkedsv.py", line 47, in main
    detect_increased_fragment_ends(args, dbo_args, endpoint_args)
  File "/home/lucab/LinkedSV/linkedsv.py", line 201, in detect_increased_fragment_ends
    get_high_coverage_regions.get_high_coverage_regions(args, dbo_args, endpoint_args)
  File "/home/lucab/LinkedSV/scripts/get_high_coverage_regions.py", line 52, in get_high_coverage_regions
    frm = Fragment(line)
  File "/home/lucab/LinkedSV/scripts/fragment.py", line 14, in __init__
    self.tid, self.start, self.end, self.length, self.bcd, self.frag_id, self.num_reads, self.hp0, self.hp1, self.hp2, self.map_pos, self.map_qual = attr_list[0:12]
ValueError: not enough values to unpack (expected 12, got 11)

Do you think this is releated to the absence of HP tag or to other possible reasons?

Thanks in advance!

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