LMAT2multi-fastsummaryTable.pl read count errors #8
Description
When I run LMAT2mult-fastsummaryTable.pl, both with and without 'megan' in the output file name, the script uses the number of threads as the total number of sequences. For example, I ran each of 24 samples through run_rl.sh with 40 threads and the resulting summary table in megan format has the following headers:
@Creator LMAT @CreationDate Tue Jul 24 21:31:18 UTC 2018 @ContentType Summary4 @Names KLF-01 KLF-02 KLF-03 KLF-04 KLF-05 KLF-06 KLF-07 KLF-08 KLF-09 KLF-10 KLF-11 KLF-12 KLF-13 KLF-14 KLF-15 KLF-16 KLF-17 KLF-18 KLF-19 KLF-20 KLF-21 KLF-22 KLF-23 KLF-24 @Sizes 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 @TotalReads 960 @Algorithm Taxonomy lmat
The log file for the run_rl.sh command is in the same folder as the .fastsummary file, so I'm not sure why I am not getting the read counts for each sample (which are significantly larger than 40).