Dear Sirs/Mesdames
Recently I am trying to treat my data from the Miseq sequencing by following the Mothur Miseq SOP. It went quite fluently until I was in the dist.seqs command. It seems taking a lot of computing power to finish it with a big data (the trim.contigs.fasta is 6.16 GB). Thus, I switched it to a cloud server with more processors to process this step. I linked it with the terminal and setup mothur working environment there. I tested it with another command and it went well. I started to run the dist.seqs command using that cloud system. It’s a linux environment.
However, the terminal revealed “broken pipe” to me several times. Once it happened, the running program was stopped. To prevent the broken pipe happens again, I tried to set up the nohup function by putting a nohup program to the directory where mothur executable file is. Then tried several commands like:
prompt$ nohup ./mothur “#dist.seqs(fasta=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.20, processors=20)†&
or
prompt$ nohup mothur “#dist.seqs(fasta=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.20, processors=20)†&
and they always gave me the error message like:
-bash: syntax error near unexpected token `(’
It seems that I cannot use ( without get into the mothur environment.
And if I get into mothur’s executable file, and use the command like:
mothur > nohup ./mothur dist.seqs(fasta=file.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.20, processors=20) &
And of course it showed me a list of the commands that I can use, not including nohup.
I am wondering if I can do something for it and don’t let the broken pipe happens again; thus, the program can finish its work without being interrupted.
Thank you for your consideration!
Best Regards,
Chih