pileup CLI parse failure

[aadali]

When I used this command: modkit pileup --reference ../../references/all_5mers.fa --bgzf --modified-bases C:m ../control_rep2.sorted.bam ./control_rep2.bedMethy.gz, it failed.

But when I put --bgzf after --modified-bases C:m, just like this: modkit pileup --reference ../../references/all_5mers.fa --modified-bases C:m --bgzf ../control_rep2.sorted.bam ./control_rep2.bedMethy.gz it worked

[ArtRand]

Hello @aadali,

Unfortunately, this is a consequence of having space-separated arguments and positional arguments. In --modified-bases C:m ../path/to/input the path is interpreted as another argument to --modified-bases. I suggest putting the positional arguments together at either the start or the end of the command.