mothur

Pre.cluster Blanks and segmentation errors

Hello again,
Wonder if you could tell me what Im doing wrong please. Mothur stopping at pre.cluster step.

mothur "#set.dir(input=/home/n/nb326/miniconda3/envs/batch/01_rawdata, output=/home/n/nb326/miniconda3/envs/batch/03_preprocess);  make.file(inputdir=/home/n/nb326/miniconda3/envs/batch/01_rawdata, type=gz, prefix=abps); make.contigs(file=/home/n/nb326/miniconda3/envs/batch/01_rawdata/abps.files, oligos=/home/n/nb326/miniconda3/envs/batch/01_rawdata/abps.oligos, pdiffs=1); summary.seqs(fasta=current)"

mothur "#screen.seqs(fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.fasta, group=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.contigs.groups, summary=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.summary,maxambig=0, minlength=252, maxlength=254, maxhomop=8); summary.seqs(fasta=current); unique.seqs(fasta=current); count.seqs(name=current,group=current);summary.seqs(fasta=current,count=current); align.seqs(fasta=current,reference=/home/n/nb326/miniconda3/envs/bpsenv/silva/silva.nr_v138/silva.nr_v138.align); summary.seqs(fasta=current,count=current)"

All fine up to here (as far as I am aware) then I come to pre.cluster and it doesn’t run the whole way:

> mothur > set.dir(output=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one)
> Mothur's directories:
> outputDir=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one/
> 
> mothur > pre.cluster(fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fasta, count=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.good.count_table, diffs=4)
> 
> Using 28 processors.
> 
> /******************************************/
> Running command: split.groups(groups=B.1.raw-B.10.raw-B.11.raw-B.12.raw-B.13.raw-B.14.raw-B.2.raw-B.3.raw-B.4.raw-B.5.raw-B.6.raw-B.7.raw-B.8.raw-B.9.raw-C.1.1.raw-C.1.2.raw-C.1.3.raw-C.10.1.raw-C.10.2.raw-C.10.3.raw-C.11.1.raw-C.11.2.raw-C.11.3.raw-C.12.1.raw-C.12.2.raw-C.12.3.raw-C.13.1.raw-C.13.2.raw-C.13.3.raw-C.14.1.raw-C.14.2.raw-C.14.3.raw-C.2.1.raw-C.2.2.raw-C.2.3.raw-C.3.1.raw-C.3.2.raw-C.3.3.raw-C.4.1.raw-C.4.2.raw-C.4.3.raw-C.5.1.raw-C.5.2.raw-C.5.3.raw-C.6.1.raw-C.6.2.raw-C.6.3.raw-C.7.1.raw-C.7.3.raw-C.8.1.raw-C.8.2.raw-C.8.3.raw-C.9.1.raw-C.9.2.raw-C.9.3.raw-F.1.1.raw-F.1.2.raw-F.1.3.raw-F.10.1.raw-F.10.2.raw-F.10.3.raw-F.11.1.raw-F.11.2.raw-F.11.3.raw-F.12.1.raw-F.12.2.raw-F.12.3.raw-F.13.1.raw-F.13.2.raw-F.13.3.raw-F.14.1.raw-F.14.2.raw-F.2.1.raw-F.2.2.raw-F.2.3.raw-F.3.1.raw-F.3.2.raw-F.3.3.raw-F.4.1.raw-F.4.2.raw-F.4.3.raw-F.5.1.raw-F.5.2.raw-F.5.3.raw-F.6.1.raw-F.6.2.raw-F.6.3.raw-F.7.1.raw-F.7.2.raw-F.7.3.raw-F.8.1.raw-F.8.2.raw-F.8.3.raw-F.9.1.raw-F.9.2.raw-F.9.3.raw-SAM1.raw-SAM3.raw, fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fasta, count=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.good.count_table)
> 
> Using 28 processors.
> /******************************************/
> Running command: get.seqs(dups=f, accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.good.F.2.3.raw.count_table.accnos, fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fastaF.2.3.raw)
> /******************************************/
> Running command: get.seqs(dups=f, accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.good.B.1.raw.count_table.accnos, fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fastaB.1.raw)
> Your file does not contain any sequence from the .accnos file.
> Selected 0 sequences from your fasta file.
> 
> Output File Names:
> /home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.unique.good.filter.fastaF.2.3.pick.raw
> 
> /******************************************/
> Done.
> Your file does not contain any sequence from the .accnos file.
> Selected 0 sequences from your fasta file.
> 
> Output File Names:
> /home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.unique.good.filter.fastaB.1.pick.raw
> 
> /******************************************/
> Done.
> /******************************************/
> Running command: get.seqs(dups=f, accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.good.F.9.2.raw.count_table.accnos, fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fastaF.9.2.raw)
> /******************************************/
> Running command: get.seqs(dups=f, accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.good.F.4.1.raw.count_table.accnos, fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fastaF.4.1.raw)
> /******************************************/
> Running command: get.seqs(dups=f, accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/one/abps.trim.contigs.good.good.F.12.3.raw.count_table.accnos, fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fastaF.12.3.raw)
> [ERROR]: /home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.good.filter.fastaF.12.3.raw is blank, aborting.
> You must provide one of the following: fasta, name, group, count, alignreport, contigsreport, taxonomy, quality, fastq or listfile.
> Segmentation fault

Hello, So I tried again, with the following:

mothur “#set.dir(input=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new), output=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new); screen.seqs(fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.align, count=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.count_table, summary=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.summary, start=13862, end=23444, maxhomop=8); summary.seqs(fasta=current, count=current); filter.seqs(fasta=current, vertical=T); pre.cluster(fasta=current, count=current, diffs=4); chimera.vsearch(fasta=current, count=current, dereplicate=t); remove.seqs(fasta=current, accnos=current); summary.seqs(fasta=current, count=current); classify.seqs(fasta=current, count=current, reference=/home/n/nb326/miniconda3/envs/bpsenv/silva/silva.nr_v138/silva.nr_v138.align, taxonomy=/home/n/nb326/miniconda3/envs/bpsenv/silva/silva.nr_v138/silva.nr_v138.tax; remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Chloroplast-Mitochondria-Eukaryota); summary.tax(taxonomy=current, count=current)”

and this was the log file:

mothur > set.dir(input=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new), output=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new)
Mothur’s directories:
outputDir=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/
/home/n/nb326/miniconda3/envs/batch/03_preprocess/new)/ directory does not exist or is not writable.

mothur > screen.seqs(fasta=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.align, count=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.count_table, summary=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.unique.summary, start=13862, end=23444, maxhomop=8)
Using 28 processors.
It took 200 secs to screen 1529102 sequences, removed 3260.
/******************************************/
Running command: remove.seqs(accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.unique.bad.accnos.temp, count=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.count_table)
Removed 10763 sequences from your count file.

Output File Names:
/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.pick.count_table

/******************************************/

Output File Names:
/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.unique.good.summary
/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.unique.good.align
/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.unique.bad.accnos
/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.good.count_table

It took 300 secs to screen 1529102 sequences.

mothur > summary.seqs(fasta=current, count=current)
Using /home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.good.count_table as input file for the count parameter.
Using /home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.unique.good.align as input file for the fasta parameter.

Using 28 processors.
[ERROR]: ‘A00881_513_HVNYHDRXX_1_2227_8712_8688’ is not in your name or count file, please correct.
[ERROR]: ‘A00881_513_HVNYHDRXX_1_2117_21802_9909’ is not in your name or count file, please correct.
[ERROR]: Your count file contains 6620 unique sequences, but your fasta file contains 2. File mismatch detected, quitting command.

It took 301 seconds to run 3 commands from your script.




Detected 3 [ERROR] messages, please review.




and if I do;

mothur > remove.seqs(accnos=/home/n/nb326/miniconda3/envs/batch/03_preprocess/new/abps.trim.contigs.good.unique.bad.accnos, count=/home/n/nb326/miniconda3/envs/batch/03_preprocess/abps.trim.contigs.good.count_table)
[ERROR]: end is not in your count table. Please correct.

Sorted, was a memory issue.

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