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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!
The text was updated successfully, but these errors were encountered:
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:
Do you think this is releated to the absence of HP tag or to other possible reasons?
Thanks in advance!
The text was updated successfully, but these errors were encountered: