Hi everyone!
I would like to ask you for help because I have a problem with the cluster command.
When we try to use the clustering script (“Cluster”, which it is the last command at the end of the pipeline) we get this error message indicating that it is unable to find the “count table” file:
“[ERROR]: M01388_125_000000000-AUMO1388_125_000000000-AU7ED_1_1106_14823_13204 is not in your count_table. Please correct.”
Below you can find the whole pipeline we had been using.
How we can fix it?
Thank you very much!
Felipe
make.contigs(ffastq=Undetermined_S0_L001_R1_001.fastq, rfastq=Undetermined_S0_L001_R2_001.fastq, findex=Undetermined_S0_L001_I1_001.fastq, oligos=Oligos_file.txt, processors=12)
cutadapt -b GTGCCAGCMGCCGCGGTAA -b GGACTACHVGGGTWTCTAAT Undetermined_S0_L001_R1_001.trim.contigs.fasta > Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.fasta
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.fasta)
screen.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.fasta, summary=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.summary, minlength=252, maxhomop=8, maxambig=0, group=Undetermined_S0_L001_R1_001.contigs.groups, processors=12)
unique.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.fasta)
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.fasta)
count.seqs(name=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.names, group=Undetermined_S0_L001_R1_001.contigs.good.groups, processors=12)
align.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.fasta, reference=/media/storage1/data_bases/silva128/silva.nr_v128.align, flip=T, processors=12)
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.align, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.count_table)
screen.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.align, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.count_table, summary=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.summary, start=13862, end=23444).
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.align, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.good.count_table)
filter.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.align, vertical=T, trump=.)
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.good.count_table)
unique.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.fasta,count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.good.count_table)
pre.cluster(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.count_table, diffs=1, processors=12)
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.count_table).
chimera.uchime(fasta=current, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.count_table, dereplicate=T, processors=12)
remove.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table, accnos=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.denovo.uchime.accnos)
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table)
classify.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.fasta,count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table,reference=/media/storage1/data_bases/silva128/silva.nr_v128.ng.fasta, taxonomy=/media/storage1/data_bases/silva128/silva.nr_v128-2.tax, cutoff=80, processors=12)
remove.lineage(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.count_table, taxonomy=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.nr_v128_2.wang.taxonomy, taxon=Mitochondria-Chloroplast)
summary.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.pick.fasta, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.denovo.uchime.pick.pick.pick.count_table, processors=12)
dist.seqs(fasta=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.pick.fasta, cutoff=0.1)
cluster(column=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.dist, count=Undetermined_S0_L001_R1_001.trim.contigs.cutadapt.good.unique.good.filter.unique.precluster.pick.count_table, cutoff=0.03, method=average, processors=12)