Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
Traceback (most recent call last):
File "/home/software/jitterbug/tools/process_ND_TD.py", line 467, in
main(sys.argv[1:])
File "/home/software/jitterbug/tools/process_ND_TD.py", line 85, in main
for line in open(read_stats_file):
TypeError: coercing to Unicode: need string or buffer, NoneType found
I already checked the script itself becuase something seems to be fishy about the read_stats_file command. It seems that read_stats_file cannot be read properly. But the files is in the dir it should be. What can I do?
Hi,
I am trying to call somatic MEl insertions in my samples. Calling and filtering works so far. process_ND_TD.py does not. When I run the code
process_ND_TD.py \ --TD_F ME/jitterbug/SE_1221/SE_1221_tumor.TE_insertions_paired_clusters.filtered.gff3 \ --ND ME/jitterbug/SE_1221/SE_1221_normal.TE_insertions_paired_clusters.gff3 \ -b bam/SE_1221_normal_sorted.bam \ -o ME/jitterbug/SE_1221/test
jitterbug throws the error
Traceback (most recent call last): File "/home/software/jitterbug/tools/process_ND_TD.py", line 467, in
main(sys.argv[1:])
File "/home/software/jitterbug/tools/process_ND_TD.py", line 85, in main
for line in open(read_stats_file):
TypeError: coercing to Unicode: need string or buffer, NoneType found
I already checked the script itself becuase something seems to be fishy about the read_stats_file command. It seems that read_stats_file cannot be read properly. But the files is in the dir it should be. What can I do?
Thanks for helping!