(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: 9f2475f [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:
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