The basic "Decontamination" mode is a very specific mode that processes the output produced by another script written by Hervé Philippe. So, it is important that it works with the output exactly as produced by this script. The output logfile typically contains first the "remove_seq" command, and then a bunch of other information that is irrelevant for the Decontamination script. This can look for example as follows:
remove_seq "Trinity_Laliostoma_00002" /home/y0088753/nodework/zip/Pre_Scafos_seperated/1/20/Laliostoma_Trinity_Protein_LFlinebreaks.ali #more similar to home/y0088753/contam_test/proteome-contam/Outgroup_proteo... (118) than to home/y0088753/contam_test/proteome-ingroup/Ingroup_databa... (-1)
At present, the program does not run with this extended log file format, probably because it considers everything after "remove_seq" as part of the sequence name to be removed.
Instead the program works well with a trimmed logfile:
remove_seq "Trinity_Laliostoma_00002"
Basically, the program should be fixed so that everything after the closing quotation mark is completely ignored.
The basic "Decontamination" mode is a very specific mode that processes the output produced by another script written by Hervé Philippe. So, it is important that it works with the output exactly as produced by this script. The output logfile typically contains first the "remove_seq" command, and then a bunch of other information that is irrelevant for the Decontamination script. This can look for example as follows: remove_seq "Trinity_Laliostoma_00002" /home/y0088753/nodework/zip/Pre_Scafos_seperated/1/20/Laliostoma_Trinity_Protein_LFlinebreaks.ali #more similar to home/y0088753/contam_test/proteome-contam/Outgroup_proteo... (118) than to home/y0088753/contam_test/proteome-ingroup/Ingroup_databa... (-1)
At present, the program does not run with this extended log file format, probably because it considers everything after "remove_seq" as part of the sequence name to be removed.
Instead the program works well with a trimmed logfile: remove_seq "Trinity_Laliostoma_00002"
Basically, the program should be fixed so that everything after the closing quotation mark is completely ignored.