No output

[dcarothomas]

Running the Pipeline-16S using the following command, nextflow run, but instead of producing the output we expected according with the information in the webpage, it produced several subdirectories that all contained copies of the ~7Gb alignment file and the smaller.tax file in the command, but there was no other output.

[... metaflowmics]$ nextflow run Pipeline-16S/main.nf -profile local --reads "$HOME/dc/microbiota/sequences/reads/_R{1,2}" --referenceAln $HOME/databases/silva/v138/silva.nr_v138.align --referenceTax $HOME/databases/silva/v138/silva.nr_v138.tax

When the program finished appeared the following message. Completed at: DATE - HOUR Duration: 1m 12s CPU hours: (a few seconds) Succeeded: 1

and create the following folder:

[... metaflowmics]$ ls 16S-pipeline_outputs

Opening the folder the only output information that we received was the following, nothing more:

16S-pipeline_outputs]$ ls parameters_summary.log

I want to know if do you have any advice to try next to fix it?

Thank you so much!!

[Puumanamana]

Could you share your full .nextflow.log file? This would help understanding what happened. Also, the documentation is not up to date, you don't need to provide --referenceAln and --referenceTax anymore, it's downloaded automatically. Finally, do you have all the dependencies installed on your machine? Even if you do, it's probably better to use docker (if it's installed on your machine), using the flag -profile local,docker

[dcarothomas]

Ok, I ran it again without providing --referenceAln and --referenceTax, and yes...I have the same output. I have all the dependencies installed when I ran nextflow. On the other hand, it's not possible to try again using docker, because it's not allowed in HPC clusters.

The .nextflow.log file says:

====== Parameter summary =====

silva database : nr_v138_1 paired end : true min reads per sample : 200 min read length : 20 read truncation : 250,170 max number of expected errors : 2 quality truncation : 2 keep phix genome : false Pooling method for denoising : F min overlap for merging : 20 max mismatches for merging : 1 Percentile for start/end contig filtering : 95 Minimum contig alignment length against db : 50 Filtered taxa : Chloroplast-Mitochondria-unknown Skip subsampling : false Percentile for automatic subsampling : 10.00 Hard threshold for automatic subsampling : 1000 clustering similarity thresholds : 100,99,97 Min OTU abundace filter : 1000 Skip LULU : false Lulu ratio type : min Lulu parent/daughter min similarity : 97 Lulu parent/daughter min abundance ratio : 1 Lulu parent/daughter min co-occurrence : 1 Skip mothur database computation : false Skip unifrac computation : false Alpha diversity metrics : nseqs-sobs-chao-shannon-shannoneven Beta diversity metrics : ~ ~ ~ ~ ~ ~ ~ "parameters_summary.log" [noeol] 30L, 1671C

Alternatively, what is the appropriate syntax to achieve the desired result when invoking Nextflow?