Hello,
I’m trying to use mothur for analysis of 16S genes of Ant endobacterial DNA, following the mothur tutorial and especially the stability.bach script.
I adapted it like this:
#Just prerequiste for the run on the universit’y cluster not important
module add EcologyEvolution/mothur/1.36.1
mothur
#set input and output directories
set.dir(input=/stn4/ul/monthly/landreot/1step/Data/Input)
set.dir(output=/stn4/ul/monthly/landreot/1step/Data/Output)
#Create contigs
make.contigs(file=AntMicrobiota.file, processors=1)
#Filter
screen.seqs(fasta=current, group=current, maxambig=0, maxlength=275)
unique.seqs(fasta=AntMicrobiota.trim.contigs.good.fasta)
count.seqs(name=current, group=current)
This whole script works, but it seems that one of the make.contigs output is empty: the AntMicrobiota.contigs.groups
It causes a lot of problems in all the next stages of analysis.
In order to not have to re-do the contigs at each run, I try to launch launch the “filter” part alone, like this:
screen.seqs(fasta=AntMicrobiota.trim.contigs.fasta, group=AntMicrobiota.contigs.groups, maxambig=0, maxlength=275)
unique.seqs(fasta=AntMicrobiota.trim.contigs.good.fasta)
count.seqs(name=current, group=current)
And I got the following message:
[ERROR]: /stn4/ul/monthly/landreot/1step/Data/Output/AntMicrobiota.contigs.groups is blank, aborting.
The AntMicrobiota.file looks like this (a “tab” is present between each columns, but it doesn’t seems to pass well on the forum, sorry):
A1 Input/A1_Ant_Microbiota_L1_R1_001.fastq.gz Input/A1_Ant_Microbiota_L1_R2_001.fastq.gz
A2 Input/A2_Ant_Microbiota_L1_R1_001.fastq.gz Input/A2_Ant_Microbiota_L1_R2_001.fastq.gz
A3 Input/A3_Ant_Microbiota_L1_R1_001.fastq.gz Input/A3_Ant_Microbiota_L1_R2_001.fastq.gz
A4 Input/A4_Ant_Microbiota_L1_R1_001.fastq.gz Input/A4_Ant_Microbiota_L1_R2_001.fastq.gz
A5 Input/A5_Ant_Microbiota_L1_R1_001.fastq.gz Input/A5_Ant_Microbiota_L1_R2_001.fastq.gz
B1 Input/B1_Ant_Microbiota_L1_R1_001.fastq.gz Input/B1_Ant_Microbiota_L1_R2_001.fastq.gz
B2 Input/B2_Ant_Microbiota_L1_R1_001.fastq.gz Input/B2_Ant_Microbiota_L1_R2_001.fastq.gz
[…]
G4 Input/G4_Ant_Microbiota_L1_R1_001.fastq.gz Input/G4_Ant_Microbiota_L1_R2_001.fastq.gz
H1 Input/H1_Ant_Microbiota_L1_R1_001.fastq.gz Input/H1_Ant_Microbiota_L1_R2_001.fastq.gz
H3 Input/H3_Ant_Microbiota_L1_R1_001.fastq.gz Input/H3_Ant_Microbiota_L1_R2_001.fastq.gz
H4 Input/H4_Ant_Microbiota_L1_R1_001.fastq.gz Input/H4_Ant_Microbiota_L1_R2_001.fastq.gz