chimera and remove.seqs fail

mothur bugs
1

Hello
When opening a mothur process in C# using ProcessStartInfo info chimera fails with a tempfile error and
remove seqs runs but fails to remove any sequences from the database

chimera.uchime(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.names, group=GQY1XT001.shhh.good.groups, processors=2)
chimera.uchime(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, reference=silva.gold.ng.fasta, processors=2)

remove.seqs(accnos=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.accnos, fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.names, group=GQY1XT001.shhh.good.groups)

2

Could you send your input and log files to mothur.bugs@gmail.com?

3

Hello
Mothur doesnt create logfiles for commands issued from C# and
I’m unable to send the input files because of privacy concerns.
Also make.shared crashes too.
Thank you
Casey

4

Are you seeing the same issues when you run mothur without ProcessStartInfo?

5

Hello
No the commands work outside of C# but not inside of a C# spawned process.
Thank you
Casey

6

I sent a logfile and how to reproduce the infinate loop to mothur.bugs@gmail.com