Squire Pipeline for TE analysis

Question

[iqra]

Hi, I have encountered this problem by using squire pipeline. but this command works for pair-end data and shows this error for single-end data. before half of my jobs are done and now its shows an error. Is there a known fix for this?

squire Count -m /home/data/TE-data/Dmrt1-data/Mapping -c /home/data/TE-data/Dmrt1-data/squire_clean -o /home/data/TE-data/Dmrt1-data/counts -t /home/data/TE-data/reference -f /home/data/TE-data/reference -r 50 -n SRR1757699 -b GRCm38 -p 32

Traceback (most recent call last):
File "/home/iqra/miniconda3/envs/squire_env/bin/squire", line 10, in
sys.exit(main())
File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/cli.py", line 156, in main
subargs.func(args = subargs)
File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/Count.py", line 1683, in main
reduce_reads(paired_bed_tempfile1_sorted, paired_reduced_tempfile1,debug)
File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/Count.py", line 378, in reduce_reads
prev.line_split[15] = prev_TE_ID
UnboundLocalError: local variable 'prev_TE_ID' referenced before assignment

another error is regarding

(squire_env) iqra@bio-Super-Server:~/miniconda3/pkgs$ squire Count -m /home/data/TE-data/Dmrt1-data/Mapping -c /home/data/TE-data/Dmrt1-data/squire_clean -o /home/data/TE-data/Dmrt1-data/counts -t /home/data/TE-data/reference -f /home/data/TE-data/reference -r 50 -n SRR1757699 -b GRCm38 -p 32

Traceback (most recent call last):
  File "/home/iqra/miniconda3/envs/squire_env/bin/squire", line 10, in <module>
    sys.exit(main())
  File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/cli.py", line 156, in main
    subargs.func(args = subargs)
  File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/Count.py", line 1805, in main
    avg_fraglength=uniquecount(unique_bedfile,RepCalc_dict,read_locdict)
  File "/home/iqra/miniconda3/envs/squire_env/lib/python2.7/site-packages/squire/Count.py", line 1231, in uniquecount
    unique_fragavg=unique_fragsum/int(unique_linecount)
ZeroDivisionError: division by zero