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: A00821:155:HNNC7DSXX:1:1101:22571:2033 , A00821:155:HNNC7DSXX:1:1101:26675:3223)
ERROR: paired_stream.hpp:154 [1] inconsistent columns (ids do not match: A00821:155:HNNC7DSXX:1:1101:22571:2033 , A00821:155:HNNC7DSXX:1:1101:26675:3223) <srprism.cpp:850>
real 0m1.714s
user 0m0.543s
sys 0m1.106s
FAILED: srprism for ./tmp//bmtagger.1572261557.localhost.122477.short