# Pre.cluster Blanks and segmentation errors **URL:** \ **Category:** Commands in mothur\ **Created:** [February 19, 2021, 11:42am UTC](https://forum.mothur.org/t/pre-cluster-blanks-and-segmentation-errors/20882 "2021-02-19T11:42:39Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![natalie](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@natalie](https://forum.mothur.org/u/natalie)\ **Post date:** [February 19, 2021, 11:42am UTC](https://forum.mothur.org/t/pre-cluster-blanks-and-segmentation-errors/20882/1 "2021-02-19T11:42:39Z")
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 ``` ---
**Author:** ![natalie](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@natalie](https://forum.mothur.org/u/natalie)\ **Post date:** [February 22, 2021, 10:00am UTC](https://forum.mothur.org/t/pre-cluster-blanks-and-segmentation-errors/20882/2 "2021-02-22T10:00:51Z")
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. * * * * * * * * * ---
**Author:** ![natalie](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@natalie](https://forum.mothur.org/u/natalie)\ **Post date:** [February 22, 2021, 10:14am UTC](https://forum.mothur.org/t/pre-cluster-blanks-and-segmentation-errors/20882/3 "2021-02-22T10:14:32Z")
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. ---
**Author:** ![natalie](https://avatars.discourse-cdn.com/v4/letter/n/e9c0ed/32.png) [@natalie](https://forum.mothur.org/u/natalie)\ **Post date:** [February 25, 2021, 8:44am UTC](https://forum.mothur.org/t/pre-cluster-blanks-and-segmentation-errors/20882/4 "2021-02-25T08:44:14Z")
Sorted, was a memory issue. ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [March 7, 2021, 8:45am UTC](https://forum.mothur.org/t/pre-cluster-blanks-and-segmentation-errors/20882/5 "2021-03-07T08:45:01Z")
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