A small question about ${i}.contig_IS_hits.txt in pseudoR_single-reference.sh (line 116 and line 97)

[EUR-C]

Hello, Joshua.
I noticed an error in my log file: cut: mapping_files/0TS10.orf_mapping.filtered.sam: No such file or directory (Same error can be found in error log in this issue: #9). I found it was caused by this command: cut -f3 mapping_files/${i}.orf_mapping.filtered.sam | sort | uniq > mapping_files/${i}.contig_IS_hits.txt (line 116 in pseudoR_single-reference.sh). Specifically, the file ${i}.orf_mapping.filtered.sam was not generated by the previous commands. Besides, the output file ${i}.contig_IS_hits.txt is the same as the output file of above command (line 97 in pseudoR_single-reference.sh).
By checking the following commands, I found the file IS_hits.txt does not seem to be used in subsequent calculations. So it maybe not affect the final results, but I am not sure.
Looking forward to your reply.

[joshuakirsch]

Hi,

Sorry about the very very very slow reply. Going back to the codebase and my error messages has also confirmed that this error message should not affect anything else. I will remove that line of code in a future update. Thanks for trying the program and hope your results were informative! Let me know if there is anything else I can help with.