cancerit/NanoSeq

part Error

MariaZhi opened this issue · 3 comments

MariaZhi commented

Hello,

I am getting an Indexing error after running the part command line.

Here is my code:
singularity run ~/nanoseq/nanoseq_2.3.3.sif runNanoSeq.py -t 1 -A SC_1_U.filtered.neat.bam -B S5_1_D.filtered.bam -R GRCh38.d1.vd1.fa part -n 60

and the error I am getting:

command arguments :
{'out': '.', 'index': None, 'max_index': None, 'threads': 1, 'ref': '/oasis/tscc/scratch/mzhivagui/Glyphosate/nanoseq_analysis/GRCh38.d1.vd1/GRCh38.d1.vd1.fa', 'normal': '/oasis/tscc/scratch/mzhivagui/Glyphosate/nanoseq_analysis/SC_1_U.filtered.neat.bam', 'tumour': '/oasis/tscc/scratch/mzhivagui/Glyphosate/nanoseq_analysis/S5_1_D.filtered.bam', 'subcommand': 'part', 'jobs': 60, 'excludeBED': None, 'excludeCov': None}

Parsing coverage files

Traceback (most recent call last):
File "/opt/wtsi-cgp/bin/runNanoSeq.py", line 662, in
cc = int(iline.split('\t')[3])
IndexError: list index out of range

Here is the header of one of the nov bed files (making sure it contains 4 columns):

chr1 8100 8200 0
chr1 8200 8300 0
chr1 8300 8400 0
chr1 8400 8500 0
chr1 8500 8600 0
chr1 8600 8700 0
chr1 8700 8800 0
chr1 8800 8900 0
chr1 8900 9000 0
chr1 9000 9100 0
chr1 9100 9200 0
chr1 9200 9300 0
chr1 9300 9400 0
chr1 9400 9500 0
chr1 9500 9600 0
chr1 9600 9700 0
chr1 9700 9800 0
chr1 9800 9900 0
chr1 9900 10000 0
chr1 10000 10100 113
chr1 10100 10200 20
chr1 10200 10300 0
chr1 10300 10400 0
chr1 10400 10500 0
chr1 10500 10600 0
chr1 10600 10700 0
chr1 10700 10800 0
chr1 10800 10900 0
chr1 10900 11000 0

rulixxx commented
rulixxx commented
MariaZhi commented