Anytime I try to use the align.seqs() command I get the following error:
Unable to open SRR830918.unique.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/SRR830918.unique.fasta.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.unique.fasta. Trying mothur's executable directory /Users/meghanstern/Desktop/mothur/SRR830918.unique.fasta.
Unable to open /Users/meghanstern/Desktop/mothur/SRR830918.unique.fasta.
Unable to open SRR830918.unique.fasta
Using 8 processors.
[ERROR]: did not complete align.seqs.
Code I executed before:
mothur > get.current()
Current RAM usage: 0.00487137 Gigabytes. Total Ram: 16 Gigabytes.
Current files saved by mothur:
processors=8
Current default directories saved by mothur:
/Users/meghanstern/Desktop/mothur/
Current working directory: /Users/meghanstern/
Output File Names:
current_files.summary
mothur > pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdots=F)
Unable to open silva.bacteria.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/silva.bacteria.fasta.
Using 8 processors.
1000
1000
1000
1000
1000
1000
1000
1000
1870
1869
1870
1870
1869
1870
1869
1869
[NOTE]: no sequences were bad, removing /Users/meghanstern/Desktop/mothur/silva.bacteria.bad.accnos
It took 5 secs to screen 14956 sequences.
Output File Names:
/Users/meghanstern/Desktop/mothur/silva.bacteria.pcr.fasta
mothur > rename.file(input=silva.bacteria.pcr.fasta, new=silva.v4.fasta)
Unable to open silva.bacteria.pcr.fasta. Trying MOTHUR_FILES directory /Users/meghanstern/Desktop/mothur/silva.bacteria.pcr.fasta.
Current files saved by mothur:
fasta=/Users/meghanstern/Desktop/mothur/silva.bacteria.pcr.fasta
processors=8
mothur > summary.seqs(fasta=silva.v4.fasta)
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 13424 269 0 3 1
2.5%-tile: 1 13424 291 0 4 374
25%-tile: 1 13424 292 0 4 3740
Median: 1 13424 292 0 4 7479
75%-tile: 1 13424 292 0 5 11218
97.5%-tile: 1 13424 293 1 6 14583
Maximum: 3 13424 350 5 9 14956
Mean: 1 13424 291 0 4
# of Seqs: 14956
It took 0 secs to summarize 14956 sequences.
Output File Names:
silva.v4.summary
The files I am using are all in the same folder with mother executable. The file is also not blank. I have also uninstalled and reinstalled mother multiple times. So I don’t know what’s going wrong. Is it something I did or is it a bug?
Can you run ls from the command prompt where you are running mothur from? Also, can you post the output of running summary.seqs(fasta=SRR830918.unique.fasta)?
Hmmm. I’m not sure how summary.seqs is running on that file since the file doesn’t appear to be in the directory you are running mothur from, which appears to be your home directory. Can you use the command line to navigate to your data directory and run mothur from there?
meghanstern@MacBook-Pro ~ % ls
Applications mothur.1659036743.logfile
Desktop mothur.1659039174.logfile
Documents mothur.1659039273.logfile
Downloads mothur.1659039368.logfile
Dropbox mothur.1659039492.logfile
Library mothur.1659039653.logfile
Movies mothur.1659039908.logfile
Music mothur.1659040060.logfile
Pictures mothur.1659040207.logfile
Public mothur.1659117867.logfile
Raven Pro 1.6 mothur.1659118028.logfile
Rplot.jpeg mothur.1659118120.logfile
VirtualBox VMs mothur.1659118460.logfile
Your team Dropbox mothur.1659118529.logfile
current_files.summary mothur.1659118881.logfile
mothur.1658780734.logfile mothur.1659365856.logfile
mothur.1658780843.logfile mothur.1659365901.logfile
mothur.1658866322.logfile mothur.1659365915.logfile
mothur.1658872396.logfile mothur.1659371576.logfile
mothur.1658890571.logfile mothur.1659382848.logfile
mothur.1658891175.logfile mothur.1659383757.logfile
mothur.1658944365.logfile mothur.1659411430.logfile
mothur.1658956134.logfile mothur.1659452324.logfile
mothur.1659028277.logfile silva.v4.8mer
mothur.1659028336.logfile silva.v4.fasta
mothur.1659035658.logfile silva.v4.summary
mothur.1659036594.logfile
meghanstern@MacBook-Pro ~ % cd Desktop/mothur
meghanstern@MacBook-Pro mothur % ls
LICENSE silva.bacteria.fasta
README-2.md silva.bacteria.fasta.download
README.md silva.bacteria.gg.tax
SRR830919.fasta silva.bacteria.ncbi.tax
SRR830919.fastq silva.bacteria.rdp.tax
SRR830919.qual silva.bacteria.rdp6.tax
SRR830919.qual.summary silva.bacteria.silva.tax
SRR830919.unique.fasta silva.gold.ng.fasta
SRR830919.unique.summary silva.v4(1).fasta
SRRfiles silva.v4.fasta
current_files.summary silva.v4.summary
fasterq-dump stability.files
mothur trainset18_062020.rdp.fasta
mothur.1659118302.logfile trainset18_062020.rdp.tax
mothur.1659496637.logfile uchime
prefetch vsearch
meghanstern@MacBook-Pro mothur % ./mothur
Mac version
Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
http://www.mothur.org
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
Distributed under the GNU General Public License
Type 'help()' for information on the commands that are available
For questions and analysis support, please visit our forum at https://forum.mothur.org
Type 'quit()' to exit program
[NOTE]: Setting random seed to 19760620.
Interactive Mode
mothur > get.current()
Current RAM usage: 0.00498199 Gigabytes. Total Ram: 16 Gigabytes.
Current files saved by mothur:
processors=8
Current default directories saved by mothur:
/Users/meghanstern/Desktop/mothur/
Current working directory: /Users/meghanstern/Desktop/mothur/
Output File Names:
current_files.summary
mothur > system(ls)
LICENSE
README-2.md
README.md
SRR830919.fasta
SRR830919.fastq
SRR830919.qual
SRR830919.qual.summary
SRR830919.unique.fasta
SRR830919.unique.summary
SRRfiles
commandScreen.output
current_files.summary
fasterq-dump
mothur
mothur.1659118302.logfile
mothur.1659496637.logfile
mothur.1659496864.logfile
prefetch
silva.bacteria.fasta
silva.bacteria.fasta.download
silva.bacteria.gg.tax
silva.bacteria.ncbi.tax
silva.bacteria.rdp.tax
silva.bacteria.rdp6.tax
silva.bacteria.silva.tax
silva.gold.ng.fasta
silva.v4(1).fasta
silva.v4.fasta
silva.v4.summary
stability.files
trainset18_062020.rdp.fasta
trainset18_062020.rdp.tax
uchime
vsearch
I did what you said, but when I try to run the align.seqs() I still got the same error.
