mothur

Issue with chimera.uchime

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

http://drive5.com/uchime

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

The chimera.uchime and chimera.vsearch commands are wrapper commands for the uchime and vsearch programs. The error you are getting is from the uchime executable. I suspect it is not built to work with Catalina. Are you able to run the chimera.vsearch command? vsearch is an open source parallelized version of the uchime program, and would be a good alternative to uchime.

Thanks for your advice! I have switched to the chimera.vsearch command.

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