When I run “gff3_sort -g Cl.rename.FINAL.gff3 -og sorted.gff3”
INFO Checking GFF3 file (Cl.rename.FINAL.gff3)...
INFO Reading gff3 file...
INFO Sorting and printing out...
Traceback (most recent call last):
File "/Users/wjx/miniconda3/bin/gff3_sort", line 8, in
sys.exit(script_main())
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/bin/gff3_sort.py", line 437, in script_main
main(args.gff_file, output=args.output_gff, isoform_sort=args.isoform_sort, sorting_order=sorting_order, logger=logger_stderr, reference=args.reference)
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/bin/gff3_sort.py", line 257, in main
otherlines.extend(gff3.collect_descendants(grandchild))
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 172, in collect_descendants
collected_list.extend(self.collect_descendants(child))
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 172, in collect_descendants
collected_list.extend(self.collect_descendants(child))
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 172, in collect_descendants
collected_list.extend(self.collect_descendants(child))
[Previous line repeated 993 more times]
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 171, in collect_descendants
collected_list.append(child)
RecursionError: maximum recursion depth exceeded while calling a Python object
When I run “gff3_sort -g Cl.rename.FINAL.gff3 -og sorted.gff3”
INFO Checking GFF3 file (Cl.rename.FINAL.gff3)... INFO Reading gff3 file... INFO Sorting and printing out... Traceback (most recent call last): File "/Users/wjx/miniconda3/bin/gff3_sort", line 8, in
sys.exit(script_main())
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/bin/gff3_sort.py", line 437, in script_main
main(args.gff_file, output=args.output_gff, isoform_sort=args.isoform_sort, sorting_order=sorting_order, logger=logger_stderr, reference=args.reference)
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/bin/gff3_sort.py", line 257, in main
otherlines.extend(gff3.collect_descendants(grandchild))
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 172, in collect_descendants
collected_list.extend(self.collect_descendants(child))
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 172, in collect_descendants
collected_list.extend(self.collect_descendants(child))
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 172, in collect_descendants
collected_list.extend(self.collect_descendants(child))
[Previous line repeated 993 more times]
File "/Users/wjx/miniconda3/lib/python3.7/site-packages/gff3tool/lib/gff3/gff3.py", line 171, in collect_descendants
collected_list.append(child)
RecursionError: maximum recursion depth exceeded while calling a Python object