mothur

Problems with summary.seqs

Hello, how are you? I have a problem during an analysis of phage therapy samples, when I get to the summary.seqs section, it indicates the following error:

mothur > summary.seqs(fasta=current, count=current)
Using /home/equiroz/Artemia/stability.trim.contigs.good.good.count_table as input file for the count parameter.
Using /home/equiroz/Artemia/stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.
Using 64 processors.
[ERROR]: /home/equiroz/Artemia/stability.trim.contigs.good.unique.good.align is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.

Could someone give me some advice on this

Kind regards

It looks like you ran screen.seqs before running align.seqs. Can you send us the command syntax you used on screen.seqs? Also, it would be great if you could include the output from running summary.seqs on stability.trim.contigs.good.unique.align and stability.trim.contigs.good.unique.good.align. I think the second *.good.align will be empty.

Pat

Thank you very much for the information, I attach the command syntax that it used until reaching screen.seqs and the results you requested, because now I cannot advance in this step summary.single (shared = stability.opti_mcc.shared, cal = nseqs -coverage-sobs-npshannon-chao, subsample = XXX), thank you very much for the help, I will be waiting for your observations to be able to advance

mothur > make.file(inputdir=file, type=fastq, prefix=stability)

mothur > make.contigs(file=stability.files, processors=16)

mothur > summary.seqs(fasta=stability.trim.contigs.fasta)

mothur > screen.seqs(fasta=stability.trim.contigs.fasta,group=stability.contig.groups, maxambig=0, maxlength=275)

mothur > get.current()

mothur > summary.seqs(fasta=stability.trim.contigs.good.fasta)

mothur > summary.seqs(fasta=current)

mothur > summary.seqs()

mothur > unique.seqs(fasta=stability.trim.contigs.good.fasta)

mothur > count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)

mothur > summary.seqs(count=stability.trim.contigs.good.count_table)

mothur > align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.bacteria.fasta)

How about the output to the screen from running summary.seqs at the various stages?

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