error collectInfo.sh

[liaguiro]

Hi

I'm getting empty files after running collectInfo.sh. I think it is related to mineMicrobialData.pl.
Can you please advise on how to fix this error?

Thanks,

Lina

-- COLLECTING INFO --

INFO: organism type flag -V not specified. O(thers) assumed (default option).

• PROCESSING DETAILS
  INFO: processing NON virus data
  INFO: filtering with DEFAULT match count threshold 5.
  Can't open input file: No such file or directory at /decontaminer_out/decontaMiner_1.4/perl_scripts/mineMicrobialData.pl line 44.
  Can't open input file: No such file or directory at /decontaMiner_1.4/perl_scripts/mineMicrobialData.pl line 44.
  INFO: filtering terminated. Generating data Matrix

WARNING: No output was written Input files do not contain non-zero matches

WARNING: No output was written Input files do not contain non-zero matches
INFO: processing terminated. Generating HTML report

ERROR !! NO FILES IN THE DIRECTORY: /decontaminer_out/RESULTS/BACTERIA/COLLECTED_INFO
ERROR !! NO FILES IN THE DIRECTORY: /decontaminer_out/RESULTS/BACTERIA/COLLECTED_INFOINFO: processing terminated. Output files written in the dir decontaminer_out/RESULTS/BACTERIA/HTML_REPORTS

[amarinderthind]

Hi, there. wondering if got an empty directory (o/p) after filterBlastInfo.sh ?

[liaguiro]

No. I'm not getting empty directories or files after running filterBlastInfo.sh (for both XXX_alignments.table and
XXX_stats.txt files)

[amarinderthind]

Could you send us " a couple of rows of intermediate files and input files"? Is it paired-end data? and please share the command that you used. Thanks.