ERROR ~ Error executing process > 'concatenateFastq'

[hvanderheyden]

Hello There, I am trying your MetONTIIME pipeline with nanopore ITS amplicon sequencing As a starter I tried with a very small data set having only 5 fastq.gz files already concatenated However I keep having an error message for concatenateFastq. Please see the log file attached Many thanks for sharing the pipeline Cheers RV

[MaestSi]

Hi, I think you forgot to attach the log file. Can you also share with me the conf file and the command line you used? Best, SM

[hvanderheyden]

Hello and thank you for your answer

here are the code lines: nextflow \ -c metontiime2.conf run metontiime2.nf \ --workDir=/media/herve/10TB/Apogee/MetONTIIME/WD \ --resultsDir=/media/herve/10TB/Apogee/MetONTIIME/resultsDir \ -profile docker

and the log and conf file

nextflow.txt metontiime2.conf.txt

In the the workDir, I have 5 fastq.gz files already concatenated 1 fastq.gz file = 1 run

[MaestSi]

Hi, first I think you should also mount /media directory, in order to make it accessible to docker (by default, only /home is accessible). You could do that editing config file at line 173: containerOptions = '-v /home/:/home -v /media:/media' If you did demultiplexing (live with MinKNOW or with guppy_barcoder), and in workDir you have folders named "barcode\<XX>", with each folder containing a set of fastq files for each sample, then concatenateFastq should be set to true (line 50 of metontiime2.conf). While, if in the workDir you already have demultiplexed fastq.gz file, with each file corresponding to a sample, concatenateFastq process should be set to false. Lastly, if you haven't done demultiplexing yet (as it seems from your sentence (1 fastq.gz file = 1 run)), please do it with Guppy, and then run MetONTIIME pipeline afterwards (setting concatenateFastq process to true or to false accordingly). SM

[hvanderheyden]

ok thank you for help

Actually, I performed basecalling and demultiplexing with guppy. I have performed 5 independent runs and each concatenate fastq.gz represent one independant run These are mock community assays.

I'll let you know how it worked

RV

[MaestSi]

Hi, I just corrected a bug causing diversityAnalysis process to start before collapseTables process was completed. Please download the updated metontiime2.nf script before re-running the pipeline. SM

[MaestSi]

Hi, are there any updates on this issue? Best, SM

[hvanderheyden]

Hello Simone, yes, I managed to have your pipeline to run with my mock samples. Thank you for your help. I am not sure however that Qiime2 is working well for my datasets. In the next few days, I will play with the parameters and see how it goes. If you want I can share some results with, perhaps via email. Cheers RV

[MaestSi]

Yes, I'd be happy to have a look at them, if you want. Best, SM

[MaestSi]

Hi, I am going to close the issue. In case you have any further questions, feel free to reopen it. Best, SM