MpGAP
MpGAP copied to clipboard
Published
20 hours ago •
fmalmeida
fmalmeida
NOTE: Process `HYBRID:strategy_2_pilon (aspergillus_terreus:strategy_2)` terminated with an error exit status (137) -- Execution is retried (1)
(base) omic@omic-Precision-7920-Tower:~/funig8$ nextflow run fmalmeida/mpgap --output _ASSEMBLY --max_cpus 5 --skip_spades --input "samplesheet.yml" --unicycler_additional_parameters ' --mode conservative ' -profile docker
curl: (28) SSL connection timeout
N E X T F L O W ~ version 24.04.2
Launching `https://github.com/fmalmeida/mpgap` [happy_meninsky] DSL2 - revision: 9f2475ff11 [master]
------------------------------------------------------
fmalmeida/mpgap v3.2
------------------------------------------------------
Core Nextflow options
revision : master
runName : happy_meninsky
containerEngine : docker
container : [.*:fmalmeida/mpgap@sha256:d0c421d2caa6bfb6fbaad36b4182746485f750c82524b7b738b0d190505c8098]
launchDir : /home/omic/funig8
workDir : /home/omic/funig8/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 [- ].
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:unicycler -
executor > local (2)
[- ] SHORTREADS_ONLY:unicycler -
executor > local (7)
[- ] SHORTREADS_ONLY:unicycler -
executor > local (7)
executor > local (7)
executor > local (8)
executor > local (11)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
executor > local (14)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
executor > local (14)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
executor > local (17)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
executor > local (17)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
executor > local (18)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
executor > local (19)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
[- ] LONGREADS_ONLY:flye -
executor > local (19)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
[- ] LONGREADS_ONLY:flye -
executor > local (22)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
executor > local (23)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
executor > local (24)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
[- ] LONGREADS_ONLY:flye -
executor > local (25)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
[- ] LONGREADS_ONLY:flye -
executor > local (26)
[- ] SHORTREADS_ONLY:unicycler -
[- ] SHORTREADS_ONLY:shovill -
[- ] SHORTREADS_ONLY:megahit -
[- ] LONGREADS_ONLY:canu -
[- ] LONGREADS_ONLY:flye -
executor > local (27)
[- ] 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 -
[a2/3c8f43] HYB…gillus_terreus:strategy_1) | 0 of 1
[e7/cdbb77] HYB…gillus_terreus:strategy_1) | 1 of 1 ✔
[64/054208] HYB…gillus_terreus:strategy_2) | 0 of 1
[5f/24fa65] HYB…gillus_terreus:strategy_2) | 1 of 1 ✔
[68/c6a255] HYB…gillus_terreus:strategy_2) | 1 of 1 ✔
[3c/83e89b] HYB…gillus_terreus:strategy_2) | 1 of 1 ✔
[- ] HYBRID:strategy_2_shasta -
[- ] HYBRID:strategy_2_hifiasm -
[8b/7f6c0e] HYB…gillus_terreus:strategy_2) | 1 of 1 ✔
[44/55e4cd] HYB…gillus_terreus:strategy_2) | 4 of 8, failed: 4, retries: 4
[36/4da361] HYB…gillus_terreus:strategy_2) | 3 of 7, failed: 3, retries: 3
[29/653896] ASS…gillus_terreus:strategy_2) | 0 of 5
Plus 5 more processes waiting for tasks…
[1a/5c45fa] NOTE: Process `HYBRID:strategy_2_pilon (aspergillus_terreus:strategy_2)` terminated with an error exit status (137) -- Execution is retried (1)
