chimera.uchime "fatal" error.

Commands in mothur
1

Hi!

I am trying to run the chimera.uchime command (mothur > chimera.uchime(fasta=Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t, processors=1)

I get a couple of errors that I don´t know how to solve:

Checking sequences from Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
[ERROR]: Could not open Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.uchime.chimeras
[ERROR]: Could not open Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.count_table
[ERROR]: Could not open Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.uchime.chimerasPHORII20P
[ERROR]: Could not open Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.unique.precluster.uchime.accnosPHORII20P

uchime.exe --input Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.fil
ter.unique.precluster.temp --uchimeout Undetermined_S0_L001_R1_001.trim.contigs.
good.unique.good.filter.unique.precluster.uchime.chimerasPHORII20P

—Fatal error—
Cannot create Undetermined_S0_L001_R1_001.trim.contigs.good.unique.good.filter.u
nique.precluster.uchime.chimerasPHORII20P, errno=2 No such file or directory
[ERROR]: Could not open Undetermined_S0_L001_R1_001.trim.contigs.good.unique.goo
d.filter.unique.precluster.uchime.chimerasPHORII20P
[ERROR]: Could not open Undetermined_S0_L001_R1_001.trim.contigs.good.unique.goo
d.filter.unique.precluster.uchime.accnosPHORII20P

I am not sure why it is trying to open files that have not been created yet. I am missing some step in between?

Thanks!

1 Like
2

Weird - can you post the fasta and count_table files to dropbox/google drive and shoot me an email - pschloss at umich - telling me where the files are? I’ll take a look and get back to you. Also, reference the url of this post.

Thanks,
Pat

3

I’m not sure what’s going on - the files go through fine for me. chimera.uchime creates these temporary files. not sure what to tell you. are you out of hard drive space? do you have the necessary permissions to write to the folder?

pat

4

Hi Pat,

Thanks for taking a look. I changed my files to another folder outside from where all the rest of files were and it seems to be working now. Not sure why but at least it looks like it works.

Thanks so much!

1 Like