workflow unsuccessful #54
Description
Hi Felipe,
I'm trying to run some annotation but no process were complete successfully even the quick test. Here is the error from quick test:
Code in collapsible form (Click to show/hide)
N E X T F L O W ~ version 22.04.4
Launching `https://github.com/fmalmeida/bacannot` [boring_cajal] DSL2 - revision: af51d9d993 [master]
------------------------------------------------------
fmalmeida/bacannot v3.1.1
------------------------------------------------------
Core Nextflow options
revision : master
runName : boring_cajal
containerEngine : docker
launchDir : /choppy
workDir : /choppy/work
projectDir : /home/fiestaj/.nextflow/assets/fmalmeida/bacannot
userName : fiestaj
profile : docker,quicktest
configFiles : /home/fiestaj/.nextflow/assets/fmalmeida/bacannot/nextflow.config
Input/output options
input : https://github.com/fmalmeida/test_datasets/raw/main/bacannot_testing_samplesheets/small_dataset_samplesheet.yml
output : EXAMPLE_OUTPUT
bacannot_db : ./bacannots_dbs
Max job request options
max_cpus : 10
max_memory : 6.GB
max_time : 6.h
Resfinder optional process
resfinder_species: Other
Select/unselect tasks to be run
skip_antismash : true
skip_kofamscan : true
User custom database
custom_db : https://github.com/fmalmeida/test_datasets/raw/main/small_custom_db.fasta
ncbi_proteins : https://github.com/fmalmeida/test_datasets/raw/main/haemophilus_ncbi_proteins.txt
Generic options
tracedir : results/pipeline_info
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use fmalmeida/bacannot for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.3627669
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/fmalmeida/bacannot/blob/master/CITATIONS.md
------------------------------------------------------
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:VFDB -
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:VFDB -
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:VFDB -
executor > local (1)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:VFDB -
executor > local (2)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:VFDB -
executor > local (2)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:VFDB -
executor > local (8)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [ 0%] 0 of 1
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (9)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [ 0%] 0 of 1
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (9)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [ 0%] 0 of 1
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [ 0%] 0 of 1
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [ 0%] 0 of 1
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (11)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (11)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (11)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (12)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [ 0%] 0 of 1
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
executor > local (13)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [ 0%] 0 of 1
executor > local (14)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [ 0%] 0 of 1
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [ 0%] 0 of 1
executor > local (15)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (15)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (16)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (17)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (17)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (18)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (19)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (19)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (19)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [ 0%] 0 of 1
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [ 0%] 0 of 1
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (22)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (23)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (23)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (23)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (23)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (24)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (24)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (30)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (30)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (30)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (30)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
[bb/f929a6] process > BACANNOT:VICTORS (h_influenzae) [100%] 1 of 1 ✔
[99/254002] process > BACANNOT:PHAST (h_influenzae) [100%] 1 of 1 ✔
[5e/10f12e] process > BACANNOT:PHIGARO (h_influenzae) [100%] 1 of 1 ✔
[e0/49de8b] process > BACANNOT:PHISPY (h_influenzae) [100%] 1 of 1 ✔
[13/f34533] process > BACANNOT:ICEBERG (h_influenzae) [100%] 1 of 1 ✔
[fd/a986ef] process > BACANNOT:AMRFINDER (h_influenzae) [100%] 1 of 1 ✔
[e6/d7f31d] process > BACANNOT:CARD_RGI (h_influenzae) [100%] 1 of 1 ✔
[d6/cc2a4b] process > BACANNOT:ARGMINER (h_influenzae) [100%] 1 of 1 ✔
[e8/b3a445] process > BACANNOT:RESFINDER (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:CALL_METHYLATION -
[7e/b7194b] process > BACANNOT:REFSEQ_MASHER (h_influenzae) [100%] 1 of 1 ✔
[cf/5a1028] process > BACANNOT:DIGIS (h_influenzae) [100%] 1 of 1 ✔
[31/a63ffb] process > BACANNOT:SEQUENCESERVER (h_influenzae) [100%] 1 of 1 ✔
[59/4929a9] process > BACANNOT:GET_NCBI_PROTEIN (1) [100%] 1 of 1 ✔
[5c/cca322] process > BACANNOT:CUSTOM_DATABASE (h_influenzae) [100%] 2 of 2 ✔
[9a/0acb30] process > BACANNOT:MERGE_ANNOTATIONS (h_influenzae) [100%] 1 of 1 ✔
[d1/637dd3] process > BACANNOT:DRAW_GIS (h_influenzae) [100%] 1 of 1 ✔
[02/b4f14a] process > BACANNOT:GFF2GBK (h_influenzae) [100%] 1 of 1 ✔
[b1/e178c5] process > BACANNOT:CREATE_SQL (h_influenzae) [100%] 1 of 1 ✔
[38/a859b3] process > BACANNOT:JBROWSE (h_influenzae) [100%] 1 of 1 ✔
[d7/d872ca] process > BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae) [ 0%] 0 of 2
[39/89d577] process > BACANNOT:REPORT (h_influenzae) [ 0%] 0 of 1
Error executing process > 'BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)'
Caused by:
Process `BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/env Rscript
## Copy reports
system("cp /work/reports/* .") ;
## Remove empty files
system("rm -f input.??") ;
system("rm -f input.?") ;
## Generate Resistance Report
rmarkdown::render("report_custom_blast.Rmd", params = list( blast_id = 65 , blast_cov = 65, query = "h_influenzae", custom_blast = "h_influenzae_small_custom_db_blastn.summary.txt", blast_db = "small_custom_db", blast_gff = "input.2")) ;
Command exit status:
1
Command output:
|
| | 0%
|
|............ | 17%
inline R code fragments
|
|....................... | 33%
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
[bb/f929a6] process > BACANNOT:VICTORS (h_influenzae) [100%] 1 of 1 ✔
[99/254002] process > BACANNOT:PHAST (h_influenzae) [100%] 1 of 1 ✔
[5e/10f12e] process > BACANNOT:PHIGARO (h_influenzae) [100%] 1 of 1 ✔
[e0/49de8b] process > BACANNOT:PHISPY (h_influenzae) [100%] 1 of 1 ✔
[13/f34533] process > BACANNOT:ICEBERG (h_influenzae) [100%] 1 of 1 ✔
[fd/a986ef] process > BACANNOT:AMRFINDER (h_influenzae) [100%] 1 of 1 ✔
[e6/d7f31d] process > BACANNOT:CARD_RGI (h_influenzae) [100%] 1 of 1 ✔
[d6/cc2a4b] process > BACANNOT:ARGMINER (h_influenzae) [100%] 1 of 1 ✔
[e8/b3a445] process > BACANNOT:RESFINDER (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:CALL_METHYLATION -
[7e/b7194b] process > BACANNOT:REFSEQ_MASHER (h_influenzae) [100%] 1 of 1 ✔
[cf/5a1028] process > BACANNOT:DIGIS (h_influenzae) [100%] 1 of 1 ✔
[31/a63ffb] process > BACANNOT:SEQUENCESERVER (h_influenzae) [100%] 1 of 1 ✔
[59/4929a9] process > BACANNOT:GET_NCBI_PROTEIN (1) [100%] 1 of 1 ✔
[5c/cca322] process > BACANNOT:CUSTOM_DATABASE (h_influenzae) [100%] 2 of 2 ✔
[9a/0acb30] process > BACANNOT:MERGE_ANNOTATIONS (h_influenzae) [100%] 1 of 1 ✔
[d1/637dd3] process > BACANNOT:DRAW_GIS (h_influenzae) [100%] 1 of 1 ✔
[02/b4f14a] process > BACANNOT:GFF2GBK (h_influenzae) [100%] 1 of 1 ✔
[b1/e178c5] process > BACANNOT:CREATE_SQL (h_influenzae) [100%] 1 of 1 ✔
[38/a859b3] process > BACANNOT:JBROWSE (h_influenzae) [100%] 1 of 1 ✔
[19/4a25a6] process > BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae) [ 50%] 1 of 2, failed: 1
[39/89d577] process > BACANNOT:REPORT (h_influenzae) [ 0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)'
Caused by:
Process `BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/env Rscript
## Copy reports
system("cp /work/reports/* .") ;
## Remove empty files
system("rm -f input.??") ;
system("rm -f input.?") ;
## Generate Resistance Report
rmarkdown::render("report_custom_blast.Rmd", params = list( blast_id = 65 , blast_cov = 65, query = "h_influenzae", custom_blast = "h_influenzae_small_custom_db_blastn.summary.txt", blast_db = "small_custom_db", blast_gff = "input.2")) ;
Command exit status:
1
Command output:
|
| | 0%
|
|............ | 17%
inline R code fragments
|
|....................... | 33%
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
[bb/f929a6] process > BACANNOT:VICTORS (h_influenzae) [100%] 1 of 1 ✔
[99/254002] process > BACANNOT:PHAST (h_influenzae) [100%] 1 of 1 ✔
[5e/10f12e] process > BACANNOT:PHIGARO (h_influenzae) [100%] 1 of 1 ✔
[e0/49de8b] process > BACANNOT:PHISPY (h_influenzae) [100%] 1 of 1 ✔
[13/f34533] process > BACANNOT:ICEBERG (h_influenzae) [100%] 1 of 1 ✔
[fd/a986ef] process > BACANNOT:AMRFINDER (h_influenzae) [100%] 1 of 1 ✔
[e6/d7f31d] process > BACANNOT:CARD_RGI (h_influenzae) [100%] 1 of 1 ✔
[d6/cc2a4b] process > BACANNOT:ARGMINER (h_influenzae) [100%] 1 of 1 ✔
[e8/b3a445] process > BACANNOT:RESFINDER (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:CALL_METHYLATION -
[7e/b7194b] process > BACANNOT:REFSEQ_MASHER (h_influenzae) [100%] 1 of 1 ✔
[cf/5a1028] process > BACANNOT:DIGIS (h_influenzae) [100%] 1 of 1 ✔
[31/a63ffb] process > BACANNOT:SEQUENCESERVER (h_influenzae) [100%] 1 of 1 ✔
[59/4929a9] process > BACANNOT:GET_NCBI_PROTEIN (1) [100%] 1 of 1 ✔
[5c/cca322] process > BACANNOT:CUSTOM_DATABASE (h_influenzae) [100%] 2 of 2 ✔
[9a/0acb30] process > BACANNOT:MERGE_ANNOTATIONS (h_influenzae) [100%] 1 of 1 ✔
[d1/637dd3] process > BACANNOT:DRAW_GIS (h_influenzae) [100%] 1 of 1 ✔
[02/b4f14a] process > BACANNOT:GFF2GBK (h_influenzae) [100%] 1 of 1 ✔
[b1/e178c5] process > BACANNOT:CREATE_SQL (h_influenzae) [100%] 1 of 1 ✔
[38/a859b3] process > BACANNOT:JBROWSE (h_influenzae) [100%] 1 of 1 ✔
[d7/d872ca] process > BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae) [100%] 2 of 2, failed: 1 ✘
[39/89d577] process > BACANNOT:REPORT (h_influenzae) [ 0%] 0 of 1
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)'
Caused by:
Process `BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/env Rscript
## Copy reports
system("cp /work/reports/* .") ;
## Remove empty files
system("rm -f input.??") ;
system("rm -f input.?") ;
## Generate Resistance Report
rmarkdown::render("report_custom_blast.Rmd", params = list( blast_id = 65 , blast_cov = 65, query = "h_influenzae", custom_blast = "h_influenzae_small_custom_db_blastn.summary.txt", blast_db = "small_custom_db", blast_gff = "input.2")) ;
Command exit status:
1
Command output:
|
| | 0%
|
|............ | 17%
inline R code fragments
|
|....................... | 33%
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
[bb/f929a6] process > BACANNOT:VICTORS (h_influenzae) [100%] 1 of 1 ✔
[99/254002] process > BACANNOT:PHAST (h_influenzae) [100%] 1 of 1 ✔
[5e/10f12e] process > BACANNOT:PHIGARO (h_influenzae) [100%] 1 of 1 ✔
[e0/49de8b] process > BACANNOT:PHISPY (h_influenzae) [100%] 1 of 1 ✔
[13/f34533] process > BACANNOT:ICEBERG (h_influenzae) [100%] 1 of 1 ✔
[fd/a986ef] process > BACANNOT:AMRFINDER (h_influenzae) [100%] 1 of 1 ✔
[e6/d7f31d] process > BACANNOT:CARD_RGI (h_influenzae) [100%] 1 of 1 ✔
[d6/cc2a4b] process > BACANNOT:ARGMINER (h_influenzae) [100%] 1 of 1 ✔
[e8/b3a445] process > BACANNOT:RESFINDER (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:CALL_METHYLATION -
[7e/b7194b] process > BACANNOT:REFSEQ_MASHER (h_influenzae) [100%] 1 of 1 ✔
[cf/5a1028] process > BACANNOT:DIGIS (h_influenzae) [100%] 1 of 1 ✔
[31/a63ffb] process > BACANNOT:SEQUENCESERVER (h_influenzae) [100%] 1 of 1 ✔
[59/4929a9] process > BACANNOT:GET_NCBI_PROTEIN (1) [100%] 1 of 1 ✔
[5c/cca322] process > BACANNOT:CUSTOM_DATABASE (h_influenzae) [100%] 2 of 2 ✔
[9a/0acb30] process > BACANNOT:MERGE_ANNOTATIONS (h_influenzae) [100%] 1 of 1 ✔
[d1/637dd3] process > BACANNOT:DRAW_GIS (h_influenzae) [100%] 1 of 1 ✔
[02/b4f14a] process > BACANNOT:GFF2GBK (h_influenzae) [100%] 1 of 1 ✔
[b1/e178c5] process > BACANNOT:CREATE_SQL (h_influenzae) [100%] 1 of 1 ✔
[38/a859b3] process > BACANNOT:JBROWSE (h_influenzae) [100%] 1 of 1 ✔
[d7/d872ca] process > BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae) [100%] 2 of 2, failed: 1 ✘
[39/89d577] process > BACANNOT:REPORT (h_influenzae) [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)'
Caused by:
Process `BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/env Rscript
## Copy reports
system("cp /work/reports/* .") ;
## Remove empty files
system("rm -f input.??") ;
system("rm -f input.?") ;
## Generate Resistance Report
rmarkdown::render("report_custom_blast.Rmd", params = list( blast_id = 65 , blast_cov = 65, query = "h_influenzae", custom_blast = "h_influenzae_small_custom_db_blastn.summary.txt", blast_db = "small_custom_db", blast_gff = "input.2")) ;
Command exit status:
1
Command output:
|
| | 0%
|
|............ | 17%
inline R code fragments
|
|....................... | 33%
executor > local (31)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[27/c088e7] process > BACANNOT:PROKKA (h_influenzae) [100%] 1 of 1 ✔
[90/6ee0ef] process > BACANNOT:MLST (h_influenzae) [100%] 1 of 1 ✔
[66/d54b59] process > BACANNOT:BARRNAP (h_influenzae) [100%] 1 of 1 ✔
[d5/333dbd] process > BACANNOT:COMPUTE_GC (h_influenzae) [100%] 1 of 1 ✔
[67/253774] process > BACANNOT:PLASMIDFINDER (h_influenzae) [100%] 1 of 1 ✔
[0e/7a4f9e] process > BACANNOT:PLATON (h_influenzae) [100%] 1 of 1 ✔
[51/d37196] process > BACANNOT:ISLANDPATH (h_influenzae) [100%] 1 of 1 ✔
[6f/f07f34] process > BACANNOT:VFDB (h_influenzae) [100%] 1 of 1 ✔
[bb/f929a6] process > BACANNOT:VICTORS (h_influenzae) [100%] 1 of 1 ✔
[99/254002] process > BACANNOT:PHAST (h_influenzae) [100%] 1 of 1 ✔
[5e/10f12e] process > BACANNOT:PHIGARO (h_influenzae) [100%] 1 of 1 ✔
[e0/49de8b] process > BACANNOT:PHISPY (h_influenzae) [100%] 1 of 1 ✔
[13/f34533] process > BACANNOT:ICEBERG (h_influenzae) [100%] 1 of 1 ✔
[fd/a986ef] process > BACANNOT:AMRFINDER (h_influenzae) [100%] 1 of 1 ✔
[e6/d7f31d] process > BACANNOT:CARD_RGI (h_influenzae) [100%] 1 of 1 ✔
[d6/cc2a4b] process > BACANNOT:ARGMINER (h_influenzae) [100%] 1 of 1 ✔
[e8/b3a445] process > BACANNOT:RESFINDER (h_influenzae) [100%] 1 of 1 ✔
[- ] process > BACANNOT:CALL_METHYLATION -
[7e/b7194b] process > BACANNOT:REFSEQ_MASHER (h_influenzae) [100%] 1 of 1 ✔
[cf/5a1028] process > BACANNOT:DIGIS (h_influenzae) [100%] 1 of 1 ✔
[31/a63ffb] process > BACANNOT:SEQUENCESERVER (h_influenzae) [100%] 1 of 1 ✔
[59/4929a9] process > BACANNOT:GET_NCBI_PROTEIN (1) [100%] 1 of 1 ✔
[5c/cca322] process > BACANNOT:CUSTOM_DATABASE (h_influenzae) [100%] 2 of 2 ✔
[9a/0acb30] process > BACANNOT:MERGE_ANNOTATIONS (h_influenzae) [100%] 1 of 1 ✔
[d1/637dd3] process > BACANNOT:DRAW_GIS (h_influenzae) [100%] 1 of 1 ✔
[02/b4f14a] process > BACANNOT:GFF2GBK (h_influenzae) [100%] 1 of 1 ✔
[b1/e178c5] process > BACANNOT:CREATE_SQL (h_influenzae) [100%] 1 of 1 ✔
[38/a859b3] process > BACANNOT:JBROWSE (h_influenzae) [100%] 1 of 1 ✔
[d7/d872ca] process > BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae) [100%] 2 of 2, failed: 1 ✘
[39/89d577] process > BACANNOT:REPORT (h_influenzae) [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)'
Caused by:
Process `BACANNOT:CUSTOM_DATABASE_REPORT (h_influenzae)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/env Rscript
## Copy reports
system("cp /work/reports/* .") ;
## Remove empty files
system("rm -f input.??") ;
system("rm -f input.?") ;
## Generate Resistance Report
rmarkdown::render("report_custom_blast.Rmd", params = list( blast_id = 65 , blast_cov = 65, query = "h_influenzae", custom_blast = "h_influenzae_small_custom_db_blastn.summary.txt", blast_db = "small_custom_db", blast_gff = "input.2")) ;
Command exit status:
1
Command output:
|
| | 0%
|
|............ | 17%
inline R code fragments
|
|....................... | 33%
label: setup (with options)
List of 1
$ include: logi FALSE
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
processing file: report_custom_blast.Rmd
Quitting from lines 24-95 (report_custom_blast.Rmd)
Error in `colnames<-`(`*tmp*`, value = c("Contig", "Source", "Feature", :
attempt to set 'colnames' on an object with less than two dimensions
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> colnames<-
Execution halted
Work dir:
/choppy/work/19/4a25a6a9f350f0c9e45317d122a157
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`