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).