Miseq mothur error with SOP in galaxy - Help please!

Question

[Melissa]

Is there an update for the following SOP: 16S Microbial Analysis with mothur (extended) 1 We keep getting an error after the unique.seq command.

Help!! Help! SOP update? Error after Unique.seq Help! SOP update? Error after Unique.seq

Mhayes 6d Is there an update for the following SOP: 16S Microbial Analysis with mothur (extended) 1 We keep getting an error after the unique.seq command.

Help!!

created 6d last reply 16h 12 replies

Mhayes 6d Error is fatal error: Exit code 1 ()

command lines:

 158 Soil Collection
:arrow_forward: 159 HMP_MOCK.v35.fasta
:arrow_forward: 160 silva.v4.fasta
:arrow_forward: 161 trainset9_032012.pds.fasta
:arrow_forward: 162 trainset9_032012.pds.tax
:arrow_forward: 163 Make.contigs on data 156, data 155, and others: trim.contigs.fasta
164 Make.contigs on data 156, data 155, and others: trim.contigs.qual
165 Make.contigs on data 156, data 155, and others: scrap.contigs.fasta
166 Make.contigs on data 156, data 155, and others: scrap.contigs.qual
167 Make.contigs on data 156, data 155, and others: report
168 Make.contigs on data 156, data 155, and others: group file
:arrow_forward: 169 Summary.seqs on data 163: logfile
:arrow_forward: 186 Summary.seqs on data 163: logfile
187 Summary.seqs on data 163: summary
:arrow_forward: 202 Screen.seqs on data 163: good.fasta
203 Screen.seqs on data 163: bad.accnos
204 Screen.seqs on data 163: align.report
:arrow_forward: 212 Unique.seqs on data 202: fasta
213 Unique.seqs on data 202: names
Fatal Error Exit code1 occurs here

unique.seqs(name=names.dat,fasta=fasta.dat,format=name)
Unable to open names.dat. Trying default /usr/local/bin/mothur/names.dat
Unable to open /usr/local/bin/mothur/names.dat. Trying mothur's location /usr/local/bin/mothurnames.dat
Unable to open /usr/local/bin/mothurnames.dat
[ERROR]: did not complete unique.seqs.

mothur > summary.seqs(fasta=fasta.dat,processors=6)

Using 6 processors.

Using 6 processors.

Using 6 processors.

Using 6 processors.

Using 6 processors.

Using 6 processors.

    Start   End NBases  Ambigs  Polymer NumSeqs
Minimum: 1 245 245 0 3 1
2.5%-tile: 1 253 253 0 3 19980
25%-tile: 1 253 253 0 4 199792
Median: 1 253 253 0 5 399584
75%-tile: 1 253 253 0 5 599376
97.5%-tile: 1 259 259 11 8 779188
Maximum: 1 502 502 251 251 799167
Mean: 1 254.169 254.169 0.981653 4.82242

of Seqs: 799167
Output File Names:
fasta.summary

It took 4 secs to summarize 799167 sequences.

mothur > quit

Error on screen.seq good fasta

[GenoMax]

It is unclear as to what your question is exactly about. Are you running mothur via Galaxy? If that is the case then please post this on their help forum to get help: https://help.galaxyproject.org/

If you are running this locally on command line please specify that command you are running.

[Melissa]

I have posted in their forum but I have not found a solution yet. I was posting here for an alternative help source.

I am running mother via Galaxy and I'm having issues specifically with the command line unique.seq. An error appears every time after this command.