Hi,
I’m new to mothur and still learning my way through it.
I’m using mothur v.1.42.0 in Windows for MiSeq data.
When I ran make.contigs(file=stability.files, processors=8), I get an error message:
Processing file pair C:\mothur\ITS2\ALAMINOS-TG-2_1.FASTQ.GZ - C:\mothur\ITS2\ALAMINOS-TG-2_2.FASTQ.GZ (files 1 of 55) <<<<<
Making contigs…
[WARNING]: reading √Hÿ\ ∞]█Üú,│> expected a name with @ as a leading character, ignoring read.
[WARNING]: reading Bi^è┌QΦ expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read √Hÿ\ ∞]█Üú,│> for fasta and Bi^è┌QΦ for quality, ignoring.[WARNING]: Lengths do not match for sequence √Hÿ\ ∞]█Üú,│>. Read 36 characters for fasta and 13 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? FASTQ format - Wikipedia
[WARNING]: reading √Hÿ\ ∞[╗ú¬▓}_┐Γ<èÆ─ expected a name with @ as a leading character, ignoring read.
[WARNING]: reading ╦⌐═L2o╬5╗{⌡Z{3╗#¿áâ┴¿óP expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read √Hÿ\ ∞[╗ú¬▓}_┐Γ<èÆ─ for fasta and ╦⌐═L2o╬5╗{⌡Z{3╗#¿áâ┴¿óP for quality, ignoring.[WARNING]: Lengths do not match for sequence √Hÿ\ ∞[╗ú¬▓}_┐Γ<èÆ─. Read 9 characters for fasta and 13 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? FASTQ format - Wikipedia
[ERROR]: You have 1 sequences in your forward fastq file, but 0 sequences in your reverse fastq file. Please use the list.seqs and get.seqs commands to make the files match before proceeding.
How do I use the above command(s)? I keep getting this error:
[ERROR]: Invalid command.
Valid commands are: align.check, align.seqs, amova, anosim, bin.seqs, biom.info, chimera.bellerophon, chimera.ccode, chimera.check, chimera.perseus, chimera.pintail, chimera.slayer, chimera.uchime, chimera.vsearch, chop.seqs, classify.otu, classify.seqs, classify.svm, classify.tree, clearcut, cluster, cluster.classic, cluster.fit, cluster.fragments, cluster.split, collect.shared, collect.single, consensus.seqs, cooccurrence, corr.axes, count.groups, count.seqs, create.database, degap.seqs, deunique.seqs, deunique.tree, dist.seqs, dist.shared, fastq.info, filter.seqs, filter.shared, get.commandinfo, get.communitytype, get.coremicrobiome, get.current, get.dists, get.group, get.groups, get.label, get.lineage, get.mimarkspackage, get.otulabels, get.otulist, get.oturep, get.otus, get.rabund, get.relabund, get.sabund, get.seqs, get.sharedseqs, heatmap.bin, heatmap.sim, help, homova, indicator, kruskal.wallis, lefse, libshuff, list.otulabels, list.otus, list.seqs, make.biom, make.contigs, make.fastq, make.file, make.group, make.lefse, make.lookup, make.shared, make.sra, make.table, mantel, merge.count, merge.files, merge.groups, merge.otus, merge.sfffiles, merge.taxsummary, metastats, mgcluster, mimarks.attributes, nmds, normalize.shared, otu.association, otu.hierarchy, pairwise.seqs, parse.list, parsimony, pca, pcoa, pcr.seqs, phylo.diversity, phylotype, pre.cluster, primer.design, quit, rarefaction.shared, rarefaction.single, remove.dists, remove.groups, remove.lineage, remove.otulabels, remove.otus, remove.rare, remove.seqs, rename.file, rename.seqs, reverse.seqs, screen.seqs, sens.spec, seq.error, set.current, set.dir, set.logfile, set.seed, sff.multiple, sffinfo, shhh.flows, shhh.seqs, sort.seqs, sparcc, split.abund, split.groups, sub.sample, summary.qual, summary.seqs, summary.shared, summary.single, summary.tax, system, tree.shared, trim.flows, trim.seqs, unifrac.unweighted, unifrac.weighted, unique.seqs, venn.
[ERROR]: did not complete list.seq.
I read some threads in the forum but I keep getting more confused. Please help! Thank you very much.