sajjadasaf commented 1 month ago

(mpgap-3.2) omic@omic-Precision-7920-Tower:~/Downloads/assembly$ nextflow run fmalmeida/mpgap --output _ASSEMBLY --max_cpus 5 --skip_spades --input "samplesheet.yml" --unicycler_additional_parameters ' --mode conservative ' -profile docker

N E X T F L O W ~ version 24.04.2

Launching https://github.com/fmalmeida/mpgap [mighty_mirzakhani] DSL2 - revision: 9f2475ff11 [master]

fmalmeida/mpgap v3.2

Core Nextflow options revision : master runName : mighty_mirzakhani containerEngine : docker container : [.*:fmalmeida/mpgap@sha256:d0c421d2caa6bfb6fbaad36b4182746485f750c82524b7b738b0d190505c8098] launchDir : /home/omic/Downloads/assembly workDir : /home/omic/Downloads/assembly/work projectDir : /home/omic/.nextflow/assets/fmalmeida/mpgap userName : omic profile : docker configFiles : /home/omic/.nextflow/assets/fmalmeida/mpgap/nextflow.config

Input/output options input : samplesheet.yml output : _ASSEMBLY

Computational options start_asm_mem : 20 GB max_cpus : 5 max_memory : 40 GB

Turn assemblers and modules on/off skip_spades : true

Software' additional parameters unicycler_additional_parameters: --mode conservative

Generic options tracedir : _ASSEMBLY/pipeline_info

!! Only displaying parameters that differ from the pipeline defaults !!

If you use fmalmeida/mpgap for your analysis please cite:

The pipeline https://doi.org/10.12688/f1000research.139488.1
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/fmalmeida/mpgap#citation

Launching defined workflows! By default, all workflows will appear in the console "log" message. However, the processes of each workflow will be launched based on the inputs received. You can see that processes that were not launched have an empty [- ].

executor > local (8) [- ] SHORTREADS_ONLY:unicycler - [- ] SHORTREADS_ONLY:shovill - [- ] SHORTREADS_ONLY:megahit - [- ] LONGREADS_ONLY:canu - [- ] LONGREADS_ONLY:flye - [- ] LONGREADS_ONLY:unicycler - [- ] LONGREADS_ONLY:raven - [- ] LONGREADS_ONLY:shasta - [- ] LONGREADS_ONLY:wtdbg2 - [- ] LONGREADS_ONLY:hifiasm - [- ] LONGREADS_ONLY:medaka - [- ] LONGREADS_ONLY:nanopolish - [- ] LONGREADS_ONLY:gcpp - [8c/80f386] HYBRID:strategy_1_unicycler (ecoli_30X:strategy_1) [ 0%] 0 of 1 [7c/ee2d18] HYBRID:strategy_1_haslr (ecoli_30X:strategy_1) [100%] 1 of 1, failed: 1 ✘ [1c/7053ec] HYBRID:strategy_2_canu (ecoli_30X:strategy_2) [ 0%] 0 of 1 [3c/9be87a] HYBRID:strategy_2_flye (ecoli_30X:strategy_2) [ 0%] 0 of 1 ✔ executor > local (8) [- ] SHORTREADS_ONLY:unicycler - [- ] SHORTREADS_ONLY:shovill - [- ] SHORTREADS_ONLY:megahit - [- ] LONGREADS_ONLY:canu - [- ] LONGREADS_ONLY:flye - [- ] LONGREADS_ONLY:unicycler - [- ] LONGREADS_ONLY:raven - [- ] LONGREADS_ONLY:shasta - [- ] LONGREADS_ONLY:wtdbg2 - [- ] LONGREADS_ONLY:hifiasm - [- ] LONGREADS_ONLY:medaka - [- ] LONGREADS_ONLY:nanopolish - [- ] LONGREADS_ONLY:gcpp - [8c/80f386] HYBRID:strategy_1_unicycler (ecoli_30X:strategy_1) [100%] 1 of 1, failed: 1 ✘ [7c/ee2d18] HYBRID:strategy_1_haslr (ecoli_30X:strategy_1) [100%] 1 of 1, failed: 1 ✘ [1c/7053ec] HYBRID:strategy_2_canu (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [3c/9be87a] HYBRID:strategy_2_flye (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [8a/54c676] HYBRID:strategy_2_unicycler (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [17/121160] HYBRID:strategy_2_raven (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [e6/4fdd45] HYBRID:strategy_2_shasta (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [- ] HYBRID:strategy_2_hifiasm - [83/f20e7f] HYBRID:strategy_2_wtdbg2 (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ executor > local (8) [- ] SHORTREADS_ONLY:unicycler - [- ] SHORTREADS_ONLY:shovill - [- ] SHORTREADS_ONLY:megahit - [- ] LONGREADS_ONLY:canu - [- ] LONGREADS_ONLY:flye - [- ] LONGREADS_ONLY:unicycler - [- ] LONGREADS_ONLY:raven - [- ] LONGREADS_ONLY:shasta - [- ] LONGREADS_ONLY:wtdbg2 - [- ] LONGREADS_ONLY:hifiasm - [- ] LONGREADS_ONLY:medaka - [- ] LONGREADS_ONLY:nanopolish - [- ] LONGREADS_ONLY:gcpp - [8c/80f386] HYBRID:strategy_1_unicycler (ecoli_30X:strategy_1) [100%] 1 of 1, failed: 1 ✘ [7c/ee2d18] HYBRID:strategy_1_haslr (ecoli_30X:strategy_1) [100%] 1 of 1, failed: 1 ✘ [1c/7053ec] HYBRID:strategy_2_canu (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [3c/9be87a] HYBRID:strategy_2_flye (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [8a/54c676] HYBRID:strategy_2_unicycler (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [17/121160] HYBRID:strategy_2_raven (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [e6/4fdd45] HYBRID:strategy_2_shasta (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [- ] HYBRID:strategy_2_hifiasm - [83/f20e7f] HYBRID:strategy_2_wtdbg2 (ecoli_30X:strategy_2) [100%] 1 of 1, failed: 1 ✘ [- ] HYBRID:strategy_2_medaka - [- ] HYBRID:strategy_2_nanopolish - [- ] HYBRID:strategy_2_gcpp - [- ] HYBRID:strategy_2_pilon - [- ] HYBRID:strategy_2_polypolish - [- ] ASSEMBLY_QC:quast - [- ] ASSEMBLY_QC:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] ASSEMBLY_QC:multiqc - Execution cancelled -- Finishing pending tasks before exit Pipeline completed at: 2024-06-03T08:53:15.368670472+04:00 Execution status: failed Execution duration: 5s Do not give up, we can fix it! WARN: The operator first is useless when applied to a value channel which returns a single value by definition ERROR ~ Error executing process > 'HYBRID:strategy_2_wtdbg2 (ecoli_30X:strategy_2)'

Caused by: Process HYBRID:strategy_2_wtdbg2 (ecoli_30X:strategy_2) terminated with an error exit status (127)

Command executed:

run wtdbg2

wtdbg2.pl \ -t 5 \ -x ont \ -g 4m \ -o ecoli_30X \ \ SRX5299443_30X.fastq.gz

rename results

cp ecoli_30X.cns.fa wtdbg2_assembly.fasta

get version

--version command does not exist

cat <<-END_VERSIONS > versions.yml "HYBRID:strategy_2_wtdbg2": wtdbg2: 2.5 END_VERSIONS

Command exit status: 127

Command output: (empty)

Command error: .command.run: line 296: docker: command not found

Work dir: /home/omic/Downloads/assembly/work/83/f20e7fb57111d1073362c72536c288

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

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

fmalmeida commented 1 month ago

Hi @sajjadasaf , Thanks for trying the pipeline. By the error, it seems you do not have Docker installed in your computer.

Is that the case?

Cheers.

sajjadasaf commented 1 month ago

Thank you for your help. yes docker was the issue.

fmalmeida commented 1 month ago

Nice. I will close the issue then. Thanks.

fmalmeida / MpGAP

ERROR ~ Error executing process > 'HYBRID:strategy_2_wtdbg2 (ecoli_30X:strategy_2)' #76