Simone Maestri

icon indicating a website link http://www.cattaneolab.it/?lang=en icon indicating an email [email protected]

icon company Università degli Studi di Milano icon location Milano, Italy icon location I'm a Biomedical Engineer and Ph. D. in Biotechnology now working as a postdoc at University of Milan

Results 42 comments of Simone Maestri

Looking for a pre-taxonomic assignment OTU table

Hi, I think what you are referring to is the ${params.resultsDir}/derepSeq/rep-seqs.qza file. You can tune **clusteringIdentity** parameter to change the minimum alignment identity within each cluster (= OTU). For example,...

Looking for a pre-taxonomic assignment OTU table

Close due to inactivity. Feel free to reopen it, in case you have any further issues. Best, SM

Looking for a pre-taxonomic assignment OTU table

Hi @hpeter0803, please refer to the previous comment, and, in case you have any issues, please let me know. SM

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

Hi, I think you may have forgotten to mount /share folder. Moreover, remember to use full paths for dbSequenceFasta and dbSequenceTaxonomy. Best, SM

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

Did you specify full paths for fasta and tsv files and also for singularity cache dir? SM

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

Please attach here .conf file (in case of troubles uploading, add .txt suffix) SM

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

I just noticed you also forgot to close apex for `dbSequencesFasta` parameter. `dbSequencesFasta="16S.fasta` Please check you fixed this. SM

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

If you look into `taxonomyVisualization `or into `assignTaxonomy` folders, can you upload qzv files to [QIIME2 View](https://view.qiime2.org/) and check whether all reads were actually unclassified or if it is an...

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

I think the problem is the file is gz compressed. Please, decompress it and retry. Best, SM

concatenateFastq process wouldn't recognize fastq.gz file in the working directory

Hi, as you reported, the error is due to the fact there are some sequences in the fasta file that are not available in the taxonomy tsv file. As far...