Hi All,
I have been trying to run the Costello stool analysis on windows version 1.29.0 (64-bit version) on windows 7. I am encountering some rather unusual errors
and I am not sure what is going on. Oddly, I am able to run the analysis with version-1.29.0 on linux with no errors and I hardly have any issues with mothur on linux. Personally, I prefer the linux version (so things are working out great for me!!!),but I am trying to help another grad student learn mothur and they prefer to use the windows version.
Basically, every time I get to the screen.seqs command it indicates that reads are missing from my group file (I get a huge list). Oddly, I can grep these sequence
names out of all of my group files generated during the analysis (stool.groups, stool.good.groups), so I am not sure why mothur is telling me they are missing.If I ignore this warning,and proceed with the analysis anyway, mothur eventually crashes when I get to the pre.cluster step.
Anybody ever encountered a similar problem running on windows? Could I be running into memory limitations or something? I have 4 Gb RAM on my windows computer. Many thanks and all the best,
Erin
Windows version
Running 64Bit Version
mothur v.1.29.0
Last updated: 1/14/2013
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
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
Type ‘quit()’ to exit program
Interactive Mode
mothur > set.dir(input=.) Mothur's directories: inputDir=C:\\Users\\Erin\\Desktop\\SOPData\\CostelloData\\
mothur > trim.seqs(fasta=stool.fasta, oligos=stool.oligos, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, processors=2)
Using 2 processors.
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Appending files from process 1
Group count:
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M11Fcsw 589
M12Fcsw 746
M13Fcsw 1773
M14Fcsw 1642
M21Fcsw 1683
M22Fcsw 1505
M23Fcsw 1805
M24Fcsw 1483
M41Fcsw 2018
M42Fcsw 1867
M43Fcsw 1611
M44Fcsw 1840
Total of all groups is 37124
Output File Names:
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.fasta
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.scrap.fasta
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.groups
mothur > summary.seqs(fasta=stool.trim.fasta)
Using 2 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 150 150 0 3 1
2.5%-tile: 1 210 210 0 4 929
25%-tile: 1 226 226 0 5 9282
Median: 1 234 234 0 5 18563
75%-tile: 1 241 241 0 5 27844
97.5%-tile: 1 254 254 0 6 36196
Maximum: 1 340 340 0 6 37124
Mean: 1 232.767 232.767 0 4.96205
of Seqs: 37124
Output File Names:
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.summary
mothur > unique.seqs(fasta=stool.trim.fasta) 1000 637 2000 1255 3000 1799 4000 2257 5000 2723 6000 3353 7000 3909 8000 4464 9000 4944 10000 5427 11000 5890 12000 6367 13000 6852 14000 7325 15000 7754 16000 8096 17000 8504 18000 8886 19000 9345 20000 9777 21000 10265 22000 10724 23000 11164 24000 11646 25000 12097 26000 12485 27000 12934 28000 13380 29000 13818 30000 14273 31000 14767 32000 15234 33000 15688 34000 16178 35000 16646 36000 17121 37000 17567 37124 17626
Output File Names:
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.names
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.fasta
mothur > summary.seqs(fasta=stool.trim.unique.fasta)
Using 2 processors.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.names which seems to match C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.fasta.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 150 150 0 3 1
2.5%-tile: 1 209 209 0 4 441
25%-tile: 1 225 225 0 5 4407
Median: 1 234 234 0 5 8814
75%-tile: 1 241 241 0 5 13220
97.5%-tile: 1 254 254 0 6 17186
Maximum: 1 340 340 0 6 17626
Mean: 1 232.763 232.763 0 4.95297
of Seqs: 17626
Output File Names:
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.summary
mothur > align.seqs(candidate=stool.trim.unique.fasta, template=silva.bacteria.fasta, processors=2)
Using 2 processors.
Reading in the C:\Users\Erin\Desktop\SOPData\CostelloData\silva.bacteria.fasta template sequences… DONE.
It took 140 to read 14956 sequences.
Aligning sequences from C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.fasta …
Reading in the C:\Users\Erin\Desktop\SOPData\CostelloData\silva.bacteria.fasta template sequences… 100
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DONE.
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It took 453 secs to align 17626 sequences.
Output File Names: C:\\Users\\Erin\\Desktop\\SOPData\\CostelloData\\stool.trim.unique.align C:\\Users\\Erin\\Desktop\\SOPData\\CostelloData\\stool.trim.unique.align.report
mothur > summary.seqs(fasta=stool.trim.unique.align)
Using 2 processors.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.names which seems to match C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.align.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1044 6332 150 0 3 1
2.5%-tile: 1726 6333 209 0 4 441
25%-tile: 1784 6333 225 0 5 4407
Median: 1795 6333 234 0 5 8814
75%-tile: 2037 6333 241 0 5 13220
97.5%-tile: 2080 6333 254 0 6 17186
Maximum: 3660 6334 310 0 6 17626
Mean: 1878.77 6332.99 232.76 0 4.95297
of Seqs: 17626
Output File Names:
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.summary
mothur > screen.seqs(fasta=stool.trim.unique.align, name=stool.trim.names, group=stool.groups, minlength=150, end=6333, processors=2)
Using 2 processors.
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Your groupfile does not include the sequence F11Fcsw_466457 please correct.
Your groupfile does not include the sequence F13Fcsw_209634 please correct.
Your groupfile does not include the sequence F13Fcsw_243841 please correct.
Your groupfile does not include the sequence F13Fcsw_2878 please correct.
Your groupfile does not include the sequence F14Fcsw_241198 please correct.
Your groupfile does not include the sequence F14Fcsw_58192 please correct.
Your groupfile does not include the sequence F21Fcsw_507537 please correct.
Your groupfile does not include the sequence F21Fcsw_64253 please correct.
Your groupfile does not include the sequence F21Fcsw_83820 please correct.
Your groupfile does not include the sequence F23Fcsw_14601 please correct.
Your groupfile does not include the sequence F23Fcsw_158211 please correct.
Your groupfile does not include the sequence F23Fcsw_18413 please correct.
Your groupfile does not include the sequence F23Fcsw_200222 please correct.
Your groupfile does not include the sequence F23Fcsw_218429 please correct.
Your groupfile does not include the sequence F23Fcsw_244638 please correct.
Your groupfile does not include the sequence F23Fcsw_42314 please correct.
Your groupfile does not include the sequence F23Fcsw_47060 please correct.
Your groupfile does not include the sequence F23Fcsw_97157 please correct.
Your groupfile does not include the sequence F24Fcsw_105949 please correct.
Your groupfile does not include the sequence F24Fcsw_208707 please correct.
Your groupfile does not include the sequence F24Fcsw_26252 please correct.
Your groupfile does not include the sequence F24Fcsw_272213 please correct.
Your groupfile does not include the sequence F31Fcsw_229862 please correct.
Your groupfile does not include the sequence F32Fcsw_156373 please correct.
Your groupfile does not include the sequence F32Fcsw_187456 please correct.
Your groupfile does not include the sequence F32Fcsw_242093 please correct.
Your groupfile does not include the sequence F32Fcsw_289329 please correct.
Your groupfile does not include the sequence F33Fcsw_151843 please correct.
Your groupfile does not include the sequence F33Fcsw_221795 please correct.
Your groupfile does not include the sequence F33Fcsw_23803 please correct.
Your groupfile does not include the sequence F34Fcsw_173974 please correct.
Your groupfile does not include the sequence F34Fcsw_207590 please correct.
Your groupfile does not include the sequence F34Fcsw_218305 please correct.
Your groupfile does not include the sequence M11Fcsw_15998 please correct.
Your groupfile does not include the sequence M11Fcsw_51639 please correct.
Output File Names:
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.good.align
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.unique.bad.accnos
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.trim.good.names
C:\Users\Erin\Desktop\SOPData\CostelloData\stool.good.groups
It took 116 secs to screen 17626 sequences.