count_folder=/output_files/repeats
EM=auto
clean_folder=squire_clean
fetch_folder=squire_fetch
name=_Aligned.sortedByCoord.out.bam
tempfolder=False
verbosity=True
pthreads=1
strandedness=0
read_length=150
build=hg38
func=<function main at 0x146cf9b8fc80>
map_folder=/output_files/alignment_intron
Traceback (most recent call last):
File "/usr/local/bin/squire", line 10, in
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/squire/cli.py", line 156, in main
subargs.func(args = subargs)
File "/usr/local/lib/python2.7/site-packages/squire/Count.py", line 1560, in main
paired_end = is_paired(bamfile,basename,tempfolder,debug)
File "/usr/local/lib/python2.7/site-packages/squire/Count.py", line 325, in is_paired
return paired
UnboundLocalError: local variable 'paired' referenced before assignment
The bam files have come from paired reads and were confirmed with flagstat.
Singularity> squire Count -m /output_files/alignment_intron -o /output_files/repeats -n _Aligned.sortedByCoord.out.bam -b hg38 -g 112 -r 150 -v start time is:2024-10-08 10:32:12.302360
Count.pyc
Script Arguments
count_folder=/output_files/repeats EM=auto clean_folder=squire_clean fetch_folder=squire_fetch name=_Aligned.sortedByCoord.out.bam tempfolder=False verbosity=True pthreads=1 strandedness=0 read_length=150 build=hg38 func=<function main at 0x146cf9b8fc80> map_folder=/output_files/alignment_intron
Traceback (most recent call last): File "/usr/local/bin/squire", line 10, in
sys.exit(main())
File "/usr/local/lib/python2.7/site-packages/squire/cli.py", line 156, in main
subargs.func(args = subargs)
File "/usr/local/lib/python2.7/site-packages/squire/Count.py", line 1560, in main
paired_end = is_paired(bamfile,basename,tempfolder,debug)
File "/usr/local/lib/python2.7/site-packages/squire/Count.py", line 325, in is_paired
return paired
UnboundLocalError: local variable 'paired' referenced before assignment
The bam files have come from paired reads and were confirmed with flagstat.