Since I updated to Catalina I have not been able to use my script which removes chimeras using uchime. Upon running chimera.uchime I get an error message about a bad CPU type. Am I missing a software update since moving to Catalina? Any help is greatly appreciated.
Thanks in advance!
Here is my log file:
Mac version
Using ReadLine,Boost,HDF5,GSL
mothur v.1.43.0
Last updated: 10/25/2019
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
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.
Batch Mode
mothur > set.dir(input = ., output = .)
Mothur’s directories:
outputDir=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/
inputDir=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/
mothur > make.file(type = fastq, prefix = stability)
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.files
mothur > make.contigs(file = stability.files, processors=8)
Using 8 processors.
Processing file pair /Users/travis/Desktop/sampled_example/DeWolfe570_S570/sampled_DeWolfe570_S570_L001_R1_001.fastq - /Users/travis/Desktop/sampled_example/DeWolfe570_S570/sampled_DeWolfe570_S570_L001_R2_001.fastq (files 1 of 1) <<<<<
Making contigs…
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Done.
It took 1 secs to assemble 4000 reads.
Group count:
sampled 4000
Total of all groups is 4000
It took 1 secs to process 4000 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.fasta
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.scrap.contigs.fasta
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.report
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.groups
mothur > summary.seqs(fasta = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.fasta as input file for the fasta parameter.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 294 294 0 4 1
2.5%-tile: 1 367 367 0 4 101
25%-tile: 1 370 370 1 4 1001
Median: 1 370 370 2 5 2001
75%-tile: 1 372 372 6 6 3001
97.5%-tile: 1 374 374 18 7 3901
Maximum: 1 600 600 51 152 4000
Mean: 1 371 371 4 5
of Seqs: 4000
It took 0 secs to summarize 4000 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.summary
mothur > screen.seqs(fasta = current, group = current, maxambig = 0, maxlength = 500, maxhomop = 6)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.fasta as input file for the fasta parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.groups as input file for the group parameter.
Using 8 processors.
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It took 0 secs to screen 4000 sequences, removed 3246.
/******************************************/
Running command: remove.seqs(accnos=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.bad.accnos.temp, group=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.groups)
Removed 3246 sequences from your group file.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.pick.groups
/******************************************/
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.fasta
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.bad.accnos
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.good.groups
It took 0 secs to screen 4000 sequences.
mothur > summary.seqs(fasta = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.fasta as input file for the fasta parameter.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 316 316 0 4 1
2.5%-tile: 1 367 367 0 4 19
25%-tile: 1 369 369 0 4 189
Median: 1 370 370 0 5 378
75%-tile: 1 371 371 0 6 566
97.5%-tile: 1 372 372 0 6 736
Maximum: 1 409 409 0 6 754
Mean: 1 369 369 0 4
of Seqs: 754
It took 0 secs to summarize 754 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.summary
mothur > unique.seqs(fasta = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.fasta as input file for the fasta parameter.
754 590
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.names
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.fasta
mothur > count.seqs(name = current, group=current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.contigs.good.groups as input file for the group parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.names as input file for the name parameter.
It took 0 secs to create a table for 754 sequences.
Total number of sequences: 754
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.count_table
mothur > summary.seqs(count = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.fasta as input file for the fasta parameter.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 316 316 0 4 1
2.5%-tile: 1 367 367 0 4 19
25%-tile: 1 369 369 0 4 189
Median: 1 370 370 0 5 378
75%-tile: 1 371 371 0 6 566
97.5%-tile: 1 372 372 0 6 736
Maximum: 1 409 409 0 6 754
Mean: 1 369 369 0 4
of unique seqs: 590
total # of seqs: 754
It took 0 secs to summarize 754 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.summary
mothur > align.seqs(fasta = current, reference =/Users/travis/Documents/microbiome_analyses/dependencies/mock_amplicons/silva.ds.run1.fasta)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.fasta as input file for the fasta parameter.
Using 8 processors.
Reading in the /Users/travis/Documents/microbiome_analyses/dependencies/mock_amplicons/silva.ds.run1.fasta template sequences… DONE.
It took 3 to read 14956 sequences.
Aligning sequences from /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.fasta …
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It took 1 secs to align 590 sequences.
[WARNING]: 11 of your sequences generated alignments that eliminated too many bases, a list is provided in /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.flip.accnos.
[NOTE]: 6 of your sequences were reversed to produce a better alignment.
It took 1 seconds to align 590 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.align
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.align.report
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.flip.accnos
mothur > summary.seqs(fasta = current, count=current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.align as input file for the fasta parameter.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 4 2 0 1 1
2.5%-tile: 1 13779 366 0 4 19
25%-tile: 1 13779 368 0 4 189
Median: 1 13779 369 0 5 378
75%-tile: 1 13779 370 0 6 566
97.5%-tile: 1 13779 371 0 6 736
Maximum: 13776 13779 372 0 6 754
Mean: 108 13687 363 0 4
of unique seqs: 590
total # of seqs: 754
It took 0 secs to summarize 754 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.summary
mothur > screen.seqs(fasta = current, count=current, summary=current, start=1, end=13779) # Eliminate reads that start after 3827 and end before 17016
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.align as input file for the fasta parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.summary as input file for the summary parameter.
Using 8 processors.
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It took 0 secs to screen 590 sequences, removed 13.
/******************************************/
Running command: remove.seqs(accnos=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.bad.accnos.temp, count=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.count_table)
Removed 13 sequences from your count file.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.pick.count_table
/******************************************/
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.summary
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.align
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.bad.accnos
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.good.count_table
It took 0 secs to screen 590 sequences.
mothur > summary.seqs(fasta = current, count = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.good.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 13779 365 0 4 1
2.5%-tile: 1 13779 366 0 4 19
25%-tile: 1 13779 369 0 4 186
Median: 1 13779 369 0 5 371
75%-tile: 1 13779 370 0 6 556
97.5%-tile: 1 13779 371 0 6 723
Maximum: 1 13779 372 0 6 741
Mean: 1 13779 369 0 4
of unique seqs: 577
total # of seqs: 741
It took 0 secs to summarize 741 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.summary
mothur > filter.seqs(fasta = current, vertical = T, trump = .)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.
Using 8 processors.
Creating Filter…
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It took 0 secs to create filter for 577 sequences.
Running Filter…
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It took 0 secs to filter 577 sequences.
Length of filtered alignment: 399
Number of columns removed: 13380
Length of the original alignment: 13779
Number of sequences used to construct filter: 577
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.filter
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.fasta
mothur > unique.seqs(fasta = current, count = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.good.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.fasta as input file for the fasta parameter.
577 574
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.count_table
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.fasta
mothur > pre.cluster(fasta = current, count = current, diffs = 2)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.fasta as input file for the fasta parameter.
Using 8 processors.
Reducing processors to 1.
/******************************************/
Running command: split.groups(groups=sampled, fasta=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.fasta, count=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.count_table)
/******************************************/
Running command: get.seqs(dups=f, accnos=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.sampled.count_table.accnos, fasta=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.fastasampled)
Selected 574 sequences from your fasta file.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.pick.fastasampled
/******************************************/
Done.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.sampled.count_table
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.sampled.fasta
/******************************************/
Processing group sampled:
sampled 0 539 35
sampled 100 377 197
sampled 200 377 197
sampled 300 377 197
sampled 400 377 197
sampled 500 377 197
sampled 574 377 197
Total number of sequences before pre.cluster was 574.
pre.cluster removed 197 sequences.
It took 0 secs to cluster 574 sequences.
Deconvoluting count table results…
377
It took 0 secs to merge 377 sequences group data.
/******************************************/
Running command: get.seqs(fasta=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.fasta, accnos=/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table.temp)
Selected 377 sequences from your fasta file.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.pick.fasta
/******************************************/
It took 0 secs to run pre.cluster.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.sampled.map
mothur > summary.seqs(fasta = current, count = current)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table as input file for the count parameter.
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 399 365 0 4 1
2.5%-tile: 1 399 366 0 4 19
25%-tile: 1 399 369 0 4 186
Median: 1 399 369 0 5 371
75%-tile: 1 399 370 0 6 556
97.5%-tile: 1 399 371 0 6 723
Maximum: 1 399 372 0 6 741
Mean: 1 399 369 0 4
of unique seqs: 377
total # of seqs: 741
It took 0 secs to summarize 741 sequences.
Output File Names:
/Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.summary
mothur > chimera.uchime(fasta = current, reference = /Users/travis/Documents/microbiome_analyses/dependencies/mock_amplicons/ds_mock_amplicons.fasta, dereplicate = t)
Using /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.
Using 8 processors.
uchime by Robert C. Edgar
This code is donated to the public domain.
Checking sequences from /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
sh: /Users/travis/Executables/mothur//uchime: Bad CPU type in executable
[ERROR]: Could not open /Users/travis/Desktop/sampled_example/DeWolfe570_S570/stability.trim.contigs.good.unique.good.filter.unique.precluster.ref.uchime.chimeras