ERROR ~ Error executing process > 'concatenateFastq'

[baotg080599]

hello, i tried run it with my fastq.gz file but it error: ERROR ~ Error executing process > 'concatenateFastq'

Caused by: Process concatenateFastq terminated with an error exit status (126)

Command executed:

mkdir -p /home/caothithuylinh/Desktop/ontimev2 mkdir -p /home/caothithuylinh/Desktop/ontimev2/concatenateFastq

barcodes_dirs=$(realpath $(find /home/caothithuylinh/Desktop/ontimev2/barcode -maxdepth 1 -mindepth 1 | grep "barcode")); echo $barcodes_dirs for b in $barcodes_dirs; do bn=$(basename $b); f=$(find $b | grep ".fastq"); zless $f | gzip > /home/caothithuylinh/Desktop/ontimev2/concatenateFastq/$bn.fastq.gz; done

Command exit status: 126

Command output: (empty)

Command error: docker: permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-jkjnUa0MU3l504IZQ171OydU": dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'.

Work dir: /home/caothithuylinh/Desktop/ontimev2/MetONTIIME/work/f5/fd7a613e78a36968b238f2d5ca5a0c

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details

please, check help me, i successfully with old version

[baotg080599]

it look error in concatenatefastq process

[MaestSi]

Hi, the error: docker: permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create?name=nxf-jkjnUa0MU3l504IZQ171OydU": dial unix /var/run/docker.sock: connect: permission denied. means that either docker daemon is not running, or you did not do post-installation steps to let it run without administrator permissions (sudo). Please try to run docker run hello-world, and have a look at this. SM

[baotg080599]

i ran docker with administrator(sudo) but it error: ERROR ~ Error executing process > 'concatenateFastq'

Caused by: Process concatenateFastq terminated with an error exit status (1)

Command executed:

mkdir -p /home/caothithuylinh/Desktop/ontimev2 mkdir -p /home/caothithuylinh/Desktop/ontimev2/concatenateFastq

barcodes_dirs=$(realpath $(find /home/caothithuylinh/Desktop/ontimev2/barcode -maxdepth 1 -mindepth 1 | grep "barcode")); echo $barcodes_dirs for b in $barcodes_dirs; do bn=$(basename $b); f=$(find $b | grep ".fastq"); zless $f | gzip > /home/caothithuylinh/Desktop/ontimev2/concatenateFastq/$bn.fastq.gz; done

Command exit status: 1

Command output: /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level6.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level4.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level5.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/sequences.qza /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level3.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/taxa-bar-plots.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level2.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level1.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/rep-seqs.qza /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level5.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/AJI298_pass_barcode01_2125d3df_42.fastq.gz /home/caothithuylinh/Desktop/ontimev2/barcode/taxonomy.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level7.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/table.qza /home/caothithuylinh/Desktop/ontimev2/barcode/demux_summary.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level7.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level1.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/taxa-bar-plots-no-Unassigned.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/table.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/collapsed_feature_tables /home/caothithuylinh/Desktop/ontimev2/barcode/taxonomy.qza /home/caothithuylinh/Desktop/ontimev2/barcode/manifest.txt /home/caothithuylinh/Desktop/ontimev2/barcode/rep-seqs.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level2.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/AJI298_pass_barcode01_2125d3df_43.fastq.gz /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level6.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level3.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/search_results.qza /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level4.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/table-no-Unassigned.qza /home/caothithuylinh/Desktop/ontimev2/barcode/AJI298_pass_barcode01_2125d3df_44.fastq.gz

Command error: /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level6.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level4.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level5.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/sequences.qza /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level3.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/taxa-bar-plots.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level2.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level1.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/rep-seqs.qza /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level5.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/AJI298_pass_barcode01_2125d3df_42.fastq.gz /home/caothithuylinh/Desktop/ontimev2/barcode/taxonomy.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level7.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/table.qza /home/caothithuylinh/Desktop/ontimev2/barcode/demux_summary.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level7.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level1.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/taxa-bar-plots-no-Unassigned.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/table.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/collapsed_feature_tables /home/caothithuylinh/Desktop/ontimev2/barcode/taxonomy.qza /home/caothithuylinh/Desktop/ontimev2/barcode/manifest.txt /home/caothithuylinh/Desktop/ontimev2/barcode/rep-seqs.qzv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level2.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/AJI298_pass_barcode01_2125d3df_43.fastq.gz /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level6.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_absfreq_level3.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/search_results.qza /home/caothithuylinh/Desktop/ontimev2/barcode/feature-table_relfreq_level4.tsv /home/caothithuylinh/Desktop/ontimev2/barcode/table-no-Unassigned.qza /home/caothithuylinh/Desktop/ontimev2/barcode/AJI298_pass_barcode01_2125d3df_44.fastq.gz

Work dir: /home/caothithuylinh/Desktop/ontimev2/MetONTIIME/work/79/94f3776154f6c871a00e76b0c67b4d

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details

[MaestSi]

You should not run docker with sudo. You should follow post-installation steps (look at the page I sent you in my previous message) in order to be able to run docker without sudo. SM

[MaestSi]

Moreover, concatenateFastq process should be set to false, if you already have one fastq.gz file for each sample. SM

[baotg080599]

how to set to false for concatenateFastq, in your tutorial i not found it?

[MaestSi]

You have to open metontiime2.conf file, and at line 50 change: concatenateFastq = true to concatenateFastq = false SM

[baotg080599]

oh, i'm sorry, thanks you so much sir

[MaestSi]

No worries, let me know if you are able to make it run. SM

[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, I am going to close this issue. In case there are any further issues, feel free to reopen it. Best, SM