mothur

Error with chimera.vsearch

I was trying to do chimera removal using chimera.search command in my 16s amplicon sequencing data. I got the following error message when the command got finished running.

It took 726 secs to check 0 sequences from group MC.
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10881.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10882.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10921.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10922.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10950.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10951.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras10957.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras11000.num.temp

Output File Names:
soil.m.s.u.g.f.p.denovo.vsearch.pick.count_table
soil.m.s.u.g.f.p.denovo.vsearch.chimeras
soil.m.s.u.g.f.p.denovo.vsearch.accnos

Can anybody help me to solve this? Thank you.

Could you post your log file?

This is the command i used to run for chimera removal

#!/bin/bash
source /opt/asn/etc/asn-bash-profiles-special/modules.sh
module load anaconda/2-4.2.0_cent
mothur “#chimera.vsearch(fasta=soil.m.s.u.g.f.p.fasta, count=soil.m.s.u.g.f.p.count_table, dereplicate=t, processors=25)”
The log file
mothur > chimera.vsearch(fasta=soil.m.s.u.g.f.p.fasta, count=soil.m.s.u.g.f.p.count_table, dereplicate=t, processors=25)

Using 25 processors.
Checking sequences from soil.m.s.u.g.f.p.fasta …

It took 751 secs to check 0 sequences from group E8.

It took 986 secs to check 0 sequences from group E9.

It took 1003 secs to check 0 sequences from group W11.

It took 1038 secs to check 0 sequences from group E6.

It took 1061 secs to check 0 sequences from group E4.

It took 1106 secs to check 0 sequences from group E7.

It took 1107 secs to check 0 sequences from group M11.
175464 here

It took 1103 secs to check 0 sequences from group E1.

It took 1146 secs to check 0 sequences from group M9.

It took 1141 secs to check 0 sequences from group W9.

It took 1155 secs to check 0 sequences from group E3.

It took 1182 secs to check 0 sequences from group M7.

It took 1188 secs to check 0 sequences from group E10.

It took 1204 secs to check 0 sequences from group E5.

It took 1221 secs to check 0 sequences from group M1.

It took 1225 secs to check 0 sequences from group W1.

It took 1260 secs to check 0 sequences from group MB.

It took 1258 secs to check 0 sequences from group W3.

It took 1282 secs to check 0 sequences from group W5.

It took 506 secs to check 0 sequences from group M8.

It took 655 secs to check 0 sequences from group MC.

It took 780 secs to check 0 sequences from group WA.

It took 791 secs to check 0 sequences from group MA.

It took 697 secs to check 0 sequences from group W4.

It took 746 secs to check 0 sequences from group M10.

It took 773 secs to check 0 sequences from group W10.

It took 808 secs to check 0 sequences from group W6.
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176698.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176701.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176725.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176726.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176730.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176734.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176738.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176769.num.temp
[ERROR]: Could not open soil.m.s.u.g.f.p.denovo.vsearch.chimeras176788.num.temp

Output File Names:
soil.m.s.u.g.f.p.denovo.vsearch.pick.count_table
soil.m.s.u.g.f.p.denovo.vsearch.chimeras
soil.m.s.u.g.f.p.denovo.vsearch.accnos

mothur > quit()




Detected 9 [ERROR] messages, please review.



What version of mothur are you running? What version of vsearch? What OS?

I am using mothur v.1.38.1 in HPC. I am running the commands in command line.