Is there an update for the following SOP: 16S Microbial Analysis with mothur (extended)
We keep getting an error after the unique.seq command.
Help!!
Error is fatal error: Exit code 1 ()
Morning, can you post your command lines?
158 Soil Collection
159 HMP_MOCK.v35.fasta
160 silva.v4.fasta
161 trainset9_032012.pds.fasta
162 trainset9_032012.pds.tax
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
169 Summary.seqs on data 163: logfile
186 Summary.seqs on data 163: logfile
187 Summary.seqs on data 163: summary
202 Screen.seqs on data 163: good.fasta
203 Screen.seqs on data 163: bad.accnos
204 Screen.seqs on data 163: align.report
212 Unique.seqs on data 202: fasta
213 Unique.seqs on data 202: names
Fatal Error Exit code1 occurs here
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
Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
The error has been logged to our team.
Hi - It looks like you are using galaxy. I think they use an older version of mothur. I’d encourage you to run the latest version of mothur on another platform.
Pat
Do you have a recommendation for a platform that would be somewhat easy to learn with an undergraduate researcher? And possibly has an SOP available? I know this is a lot to ask, but keeping my fingers crossed that you may have the answers. Thank you!!
Do you have a recommendation for a platform that would be somewhat easy to learn with an undergraduate researcher? And possibly has an SOP available? I know this is a lot to ask, but keeping my fingers crossed that you may have the answers. Thank you!!
It depends on how large the dataset is. Many people are able to process their data on a laptop. Aside from that you could try setting up an amazon web services (AWS) account
Pat
We have 63 soil samples that we extracted DNA from and sent to U of Michigan’s microbiome core. We received F and R fastq files and followed the SOP: 16S Microbial Analysis with mothur (extended)- until we ran into the unique.seq error on UseGalaxy. We are at a small liberal arts college in SC and this is an undergraduate’s research project. Unfortunately, we don’t have any other faculty or staff who can assist us with these types of issues. We are learning as we go. I don’t think we would need a web services account since our dataset is quite small. I am really unsure of the other platforms - UseGalaxy was a amazing tool suite for us to use for this project since there was an SOP. Any advice is appreciated. Thank you!!
I’d suggest running it on a laptop or desktop computer
Pat
That is what we are currently doing. Is there another platform outside of Use Galaxy that you recommend?
You can run mothur on your local windows/mac/linux computer using the command line interface that’s installed on your computer.
Pat
Okay. Thanks. I think what I’m trying to ask is if there’s an alternative to the useGalaxy tool suite for mothur. My students have spent more than one semester learning the tool suite and now we need to switch to the command line mothur program. As undergrads this is going to be a big switch for them.
So because useGalaxy’s not using the latest version of mothur, there’s not going to be a way to get around this error?
This is the error from the log file now
mothur > 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.
I’m sorry but I’ve never used Galaxy and we don’t have a collaboration with them. Perhaps you could ask the galaxy maintainers to update their version of mothur?
Pat