Dear All,

I tried to analyse paired end fastq data of Illumina using Viromescan after successfully following the instructions given in sourceforge.net (files section) and ended up getting the following error.

" ./options_parser_priv.hpp:246 [3] argument missing (missing required option paired) ERROR: ./options_parser_priv.hpp:246 [3] argument missing (missing required option paired) <srprism.cpp:850> real 0m0.008s user 0m0.002s sys 0m0.000s FAILED: srprism for viromescan_sample_D/tmp//bmtagger.1564403652.pr615-Lenovo-Legion-Y530-15ICH.27953.short "

Then, I changed line 34 of bmtagger.sh from, srprismopts="-b 100000000 -n 5 -R 0 -r 1 -M 7168" to srprismopts="-b 100000000 -n 5 -R 0 -r 1 -M 7168 -p true" because I came across the following sentence in the bmtagger,.sh script.

"notes: "You may find it necessary to create a bmtagger.conf file to specify paired or single-end searching. The file should contain the line 'srprismopts=\"-b 100000000 -n 5 -R 0 -r 1 -M 7168\"' along with '-p true' or '-p false' for paired, and single, respectively. This config file can be passed to bmtagger.sh via the '-C' option." "

After the above correction, I am getting the below error.

paired_stream.hpp:154 [1] inconsistent columns (ids do not match: M05773:20:000000000-C8WP2:1:1101:16364:6851 , M05773:20:000000000-C8WP2:1:1101:13627:8301) ERROR: paired_stream.hpp:154 [1] inconsistent columns (ids do not match: M05773:20:000000000-C8WP2:1:1101:16364:6851 , M05773:20:000000000-C8WP2:1:1101:13627:8301) <srprism.cpp:850>

Appreciate if anyone could give me a suggestion to solve this problem. Thank you!