Pre.cluster error in 1.42.0

1

Hello all -

We are running mothur version 1.42.0 on an 8 core 16 thread windows PC to test if we want to purchase our own lab computer or continue using our university’s computer cluster.

We ran a single mock community sample (MiSeq 300 bp 16S rRNA Illumina, Earth microbiome primers) which we have previously run on the cluster and on our laptop computers. When we run this sample on the 8 core, we are unable to get past the pre.cluster step because mothur unexpectedly quits. The log file appears to show that it stops after attempting to run split.groups. We have checked the memory, CPU, and disk when we perform this task, and these do not appear to be the issue. Additionally, we have run the pre.cluster step on another computer and transferred the files to continue with the SOP on the 8 core, but mothur quits after running chimera.vsearch and the log file shows it stops after attempting to run split.groups.

Any ideas what the issue could be? We have not had these issues on the other computers and the cluster, which currently have version 1.40.5 installed rather than 1.42.0.

Thank you very much for your suggestions.

2

I haven’t gotten 1.42.(any version) to work on our cluster either.

3

Can you try 1.42.3 - this was a problem that we think we solved with the more recent sub-release.

@Kendra, what does not working look like?

Pat

4

Thank you, we will try that!
-Madison

5

I have been having trouble at this step too - with version 1.42.3 (Linux version). My job had previously stopped on the chimera.uchime step. So I restarted, but with chimera.vsearch, beginning at the chimera.vsearch step. My job then stopped running before completing chimera.vsearch.
Previously I ended up using 1.39.5 to run chimera.uchime for this dataset and that worked but I’d like to run the whole batch with the latest version. Thank you!

Here’s an excerpt from my latest logfile:

mothur > chimera.vsearch(fasta=Marimba.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=Marimba.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t, processors=10)

Using 10 processors.
Checking sequences from Marimba.trim.contigs.good.unique.good.filter.unique.precluster.fasta …

/******************************************/
Running command: split.groups(groups=DNA_extraction_control_Marimba09-EMPTY_02_S159_Marimba06-EMPTY_1_S96_Marimba02-EMPTY_2_S192_Marimba02-EMPTY_S17_Marimba06-EMPTY_S192_Marimba01-EMPTY_S305_Marimba03-EMPTY_S96_Marimba01-Empty_A_Marimba14-MBR00001-MBR00002-MBR00003-MBR00004-MBR00005-MBR00006-MBR00007-MBR00008-MBR00009-MBR00010-MBR00011-MBR00012-MBR00013-MBR00014-MBR00015-MBR00016-MBR00017-MBR00018-MBR00019-MBR00020-MBR00021-MBR00022-MBR00023-MBR00024-MBR00025-MBR00026-MBR00027-MBR00028-##skipped_a_bunch_of_groups_to_fit_on forum##-zymo_D_Marimba07, fasta=Marimba.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=Marimba.trim.contigs.good.unique.good.filter.unique.precluster.count_table)

Output File Names:
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.DNA_extraction_control_Marimba09.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.DNA_extraction_control_Marimba09.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_02_S159_Marimba06.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_02_S159_Marimba06.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_1_S96_Marimba02.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_1_S96_Marimba02.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_2_S192_Marimba02.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_2_S192_Marimba02.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S17_Marimba06.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S17_Marimba06.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S192_Marimba01.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S192_Marimba01.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S305_Marimba03.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S305_Marimba03.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S96_Marimba01.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.EMPTY_S96_Marimba01.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.Empty_A_Marimba14.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.Empty_A_Marimba14.count_table
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.MBR00001.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.MBR00001.count_table

##skipping many similar lines

Marimba.trim.contigs.good.unique.good.filter.unique.precluster.zymo_D_Marimba07.fasta
Marimba.trim.contigs.good.unique.good.filter.unique.precluster.zymo_D_Marimba07.count_table

/******************************************/
Error in reading your fastafile, at position -1. Blank name.

Removing group: DNA_extraction_control_Marimba09 because all sequences have been removed.

Removing group: EMPTY_02_S159_Marimba06 because all sequences have been removed.

Removing group: EMPTY_1_S96_Marimba02 because all sequences have been removed.

Removing group: EMPTY_2_S192_Marimba02 because all sequences have been removed.

Removing group: EMPTY_S17_Marimba06 because all sequences have been removed.

Removing group: EMPTY_S192_Marimba01 because all sequences have been removed.

Removing group: EMPTY_S305_Marimba03 because all sequences have been removed.

Removing group: EMPTY_S96_Marimba01 because all sequences have been removed.

Removing group: Empty_A_Marimba14 because all sequences have been removed.

Removing group: MBR00001 because all sequences have been removed.

##skipping many similar lines

Removing group: zymo_D_Marimba07 because all sequences have been removed. ##the logfile ended here (line 20645).

6

Sorry - meant to add this to the chime discussion rather than the pre.cluster discussion: Uchime issues with 1.42.1?

7

Hi Pat, I was getting hangs and kills with 1.42.x but can’t remember which version was giving which error. I’ve restarted my test samples with 1.42.3 and will send you the log

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