fetyj
commented
2 years ago Here is two errors with two different strain I'm working with.
Closed fetyj closed 2 years ago
fetyj
commented
2 years ago Here is two errors with two different strain I'm working with.
fetyj
commented
2 years ago It seems that the errors are species dependent...
Fety
fmalmeida
commented
2 years ago Hi Fety,
All the errors are with PHIGARO. The other processes seem to be working well.
I will take a look whether some major change has hapenned with phigaro tool and if I will need to update it.
But at least it doesn't seem like some problem related to the pipeline itself but more with my phigaro installation/execution on docker.
I'll take a look 😄
fmalmeida
commented
2 years ago Do you know if the database download worked sucessfully for PHIGARO and it did not corrupted some file? While I take a look at it I would suggest that you remove the phigaro database and download again setting the pipeline to save it in the sabe directory.
It should be smart enough to only download PHIGARO as it will be the only one missing after you remove it.
fetyj
commented
2 years ago Just try to remove and download new PHIGARO databases but still get an error
fmalmeida
commented
2 years ago I will try running the example dataset and see what happens.
then we can try to understand why it happens with your dataset depending on what I get
😄
fetyj
commented
2 years ago yes I removed PHIGARO_db and download it again with --get_dbs in the same db_directory
fmalmeida
commented
2 years ago yes I removed PHIGARO_db and download it again with
--get_dbsin the same db_directory
I saw later. Haven't read it all.
My bad.
I'll take a look at it during the weekend.
Have a nice weekend:)
fetyj
commented
2 years ago Thanks, the same to you :)
fmalmeida
commented
2 years ago Hi Fety,
I just tested the workflow. It indeed had an error when custom blast output was empty, but this was a simple fix and I just updated the docker image (fmalmeida/bacannot:v3.1_renv). So please, update it before running new tests 😄
But I was not able to replicate any of your errors. As you can see below, as able to run the pipeline successfully with both the quicktest and normal test profiles:
So, this makes me think that, either it exists some problem with your dataset or with the database/command line used. I assume is the second as you weren't able to run with the test profiles as well.
I noticed that you called the workflow with --bacannot_db ./bacannots_dbs. Maybe there is a misspelling there and you meant --bacannot_db ./bacannot_dbs?
I am updating the workflow to check if inputs given actually exist to avoid misspelling problems. This will be on
v3.1.2until monday.
And if it is not a misspelling and your folder is really called ./bacannots_dbs, perhaps there is something wrong with the files, so, I made it available for you to download if wanted the very same database I used to run the tests I just screenshotted:
fetyj
commented
2 years ago Hi Felipe,
The database name was just a typo when I built it but just to make sure everything is ok I erased all of it and downloaded from above. Everything went just fine on both quicktest (when I run the ./run_server.sh -s it gives me an error Error: subscript out of bounds, and I'm still waiting for the normal test to finish but everything seems good.
Unfortunately, I was unable to successfully annotate my data as you see here
N E X T F L O W ~ version 22.04.4
Launching `https://github.com/fmalmeida/bacannot` [wise_archimedes] DSL2 - revision: af51d9d993 [master]
------------------------------------------------------
fmalmeida/bacannot v3.1.1
------------------------------------------------------
Core Nextflow options
revision : master
runName : wise_archimedes
containerEngine: docker
launchDir : /choppy
workDir : /choppy/work
projectDir : /home/fiestaj/.nextflow/assets/fmalmeida/bacannot
userName : fiestaj
profile : docker
configFiles : /home/fiestaj/.nextflow/assets/fmalmeida/bacannot/nextflow.config
Input/output options
input : bacannot_samplesheet-1769.yaml
output : 1769_bacannot
bacannot_db : ./bacannot_dbs
Max job request options
max_cpus : 10
!! 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:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
executor > local (1)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
executor > local (1)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
executor > local (2)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MLST [ 0%] 0 of 1
[- ] process > BACANNOT:BARRNAP [ 0%] 0 of 1
[- ] process > BACANNOT:COMPUTE_GC [ 0%] 0 of 1
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (8)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MLST [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (9)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [ 0%] 0 of 1
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [ 0%] 0 of 1
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [ 0%] 0 of 1
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [ 0%] 0 of 1
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [ 0%] 0 of 1
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [ 0%] 0 of 1
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [ 0%] 0 of 1
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [ 0%] 0 of 1
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [ 0%] 0 of 1
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[3d/7475f9] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[5f/060364] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[9b/2b0192] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[f4/44510c] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[5f/257afb] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:ISLANDPATH [ 0%] 0 of 1
[- ] process > BACANNOT:VFDB [ 0%] 0 of 1
[- ] process > BACANNOT:VICTORS [ 0%] 0 of 1
[- ] process > BACANNOT:PHAST [ 0%] 0 of 1
[- ] process > BACANNOT:PHIGARO [ 0%] 0 of 1
[4d/e90498] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[- ] process > BACANNOT:ICEBERG [ 0%] 0 of 1
[- ] process > BACANNOT:AMRFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:CARD_RGI [ 0%] 0 of 1
[- ] process > BACANNOT:ARGMINER [ 0%] 0 of 1
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[e0/06d669] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[b1/21bf71] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[33/efc58b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[7f/216d59] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHISPY (sthermophilus)'
Caused by:
Process `BACANNOT:PHISPY (sthermophilus)` terminated with an error exit status (1)
Command executed:
# get tool version
PhiSpy.py -v > phispy_version.txt ;
# run phispy
PhiSpy.py \
-o PhiSpy \
sthermophilus.gbk \
--color \
--output_choice 127 \
--threads 4
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Traceback (most recent call last):
File "/opt/conda/bin/PhiSpy.py", line 10, in <module>
sys.exit(run())
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 122, in run
main(sys.argv)
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/main.py", line 44, in main
args_parser.record = PhiSpyModules.SeqioFilter(filter(lambda x: len(x.seq) > args_parser.min_contig_size, SeqIO.parse(handle, "genbank")))
File "/opt/conda/lib/python3.8/site-packages/PhiSpyModules/seqio_filter.py", line 33, in __init__
for n, item in enumerate(content):
File "/opt/conda/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 73, in __next__
return next(self.records)
File "/opt/conda/lib/python3.8/site-packages/Bio/GenBank/Scanner.py", line 516, in parse_records
record = self.parse(handle, do_features)
File "/opt/conda/lib/python3.8/site-packages/Bio/GenBank/Scanner.py", line 499, in parse
if self.feed(handle, consumer, do_features):
File "/opt/conda/lib/python3.8/site-packages/Bio/GenBank/Scanner.py", line 465, in feed
self._feed_first_line(consumer, self.line)
File "/opt/conda/lib/python3.8/site-packages/Bio/GenBank/Scanner.py", line 1572, in _feed_first_line
raise ValueError("Did not recognise the LOCUS line layout:\n" + line)
ValueError: Did not recognise the LOCUS line layout:
LOCUS lcl_cluster_001_consensus_polypolish1857574 bp DNA linear
Work dir:
/choppy/work/4d/e90498a67a68ec67e45e9535cbc11d
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`normal test successful but I got an error Error: object 'name' not found with the ./run_server.sh command
fmalmeida
commented
2 years ago Thank you for the feedback. I will take a look at it during the week.
To try to figure it out what is happening with it when running with your data and with the "shiny app script" I probably messed with something when updating the Rmd files.
Probably your answer is no, but would you share your contigs so I can try to replicate? It can either be the entire fasta or a subset of them.
Can be to my email so they don't stay public
fmalmeida
commented
2 years ago Looking at this specific line of the error you shared:
Did not recognise the LOCUS line layout:
LOCUS lcl_cluster_001_consensus_polypolish1857574 bp DNA linearI believe the error you are facing with your dataset is due the fact that NCBI headers have a limit length of 16 characters. And your sequence headers are bigger than that.
While I try to figure out what happened with the shiny app I would suggest that you rename and diminish the ID of your contigs in your fasta and try again.
You can try seqkit for that.
fetyj
commented
2 years ago Hi Felipe, Thanks for helping out. So I rename my file and more analysis passed but there is still error with PHIGARO.
N E X T F L O W ~ version 22.04.4
Launching `https://github.com/fmalmeida/bacannot` [dreamy_bohr] DSL2 - revision: af51d9d993 [master]
------------------------------------------------------
fmalmeida/bacannot v3.1.1
------------------------------------------------------
Core Nextflow options
revision : master
runName : dreamy_bohr
containerEngine: docker
launchDir : /choppy
workDir : /choppy/work
projectDir : /home/fiestaj/.nextflow/assets/fmalmeida/bacannot
userName : fiestaj
profile : docker
configFiles : /home/fiestaj/.nextflow/assets/fmalmeida/bacannot/nextflow.config
Input/output options
input : bacannot_samplesheet-1769.yaml
output : 1769_bacannot
bacannot_db : ./bacannot_dbs
Max job request options
max_cpus : 10
!! 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:KOFAMSCAN -
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[- ] process > BACANNOT:PROKKA -
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
executor > local (1)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
executor > local (1)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:MLST -
[- ] process > BACANNOT:BARRNAP -
[- ] process > BACANNOT:COMPUTE_GC -
[- ] process > BACANNOT:KOFAMSCAN -
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER -
[- ] process > BACANNOT:PLATON -
executor > local (8)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (8)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (9)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (9)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (9)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [ 0%] 0 of 1
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (10)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (11)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (12)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (12)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (13)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [ 0%] 0 of 1
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (13)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (14)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[- ] process > BACANNOT:PLASMIDFINDER [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (15)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (16)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (16)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (17)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (17)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (17)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:PLATON [ 0%] 0 of 1
executor > local (18)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [ 0%] 0 of 1
executor > local (18)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [ 0%] 0 of 1
executor > local (19)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
executor > local (19)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
executor > local (20)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KOFAMSCAN [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[be/41a274] process > BACANNOT:KOFAMSCAN (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[be/41a274] process > BACANNOT:KOFAMSCAN (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[be/41a274] process > BACANNOT:KOFAMSCAN (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[02/cce239] process > BACANNOT:ISLANDPATH (sthermophilus) [100%] 1 of 1 ✔
[bf/fd24d1] process > BACANNOT:VFDB (sthermophilus) [100%] 1 of 1 ✔
[5c/906ff6] process > BACANNOT:VICTORS (sthermophilus) [100%] 1 of 1 ✔
[2b/d43309] process > BACANNOT:PHAST (sthermophilus) [100%] 1 of 1 ✔
[0e/a237fe] process > BACANNOT:PHIGARO (sthermophilus) [ 0%] 0 of 1
[9c/9bab7a] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1 ✔
[41/a6274d] process > BACANNOT:ICEBERG (sthermophilus) [100%] 1 of 1 ✔
[f5/c6cb20] process > BACANNOT:AMRFINDER (sthermophilus) [100%] 1 of 1 ✔
[eb/0cfd15] process > BACANNOT:CARD_RGI (sthermophilus) [100%] 1 of 1 ✔
[16/30413d] process > BACANNOT:ARGMINER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[b6/12d966] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[d7/019954] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1 ✔
[47/c7d59b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1 ✔
[48/dfd034] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Error executing process > 'BACANNOT:PHIGARO (sthermophilus)'
Caused by:
Process `BACANNOT:PHIGARO (sthermophilus)` terminated with an error exit status (1)
Command executed:
# activate env
source activate phigaro
# get tool version
phigaro -V > phigaro_version.txt ;
# create new config to properly load database
cp $(which config.yml) ./custom_config.yml ;
sed -i "s|CHANGE_PVOG|bacannot_dbs/phigaro_db/allpvoghmms|" ./custom_config.yml ;
HMM_BIN=$(which hmmsearch) ;
sed -i "s|CHANGE_HMMSEARCH|$HMM_BIN|" ./custom_config.yml ;
PRODIGAL_BIN=$(which prodigal) ;
sed -i "s|CHANGE_PRODIGAL|$PRODIGAL_BIN|" ./custom_config.yml ;
# run phigaro
phigaro \
-f assembly.fasta \
--config ./custom_config.yml \
-t 4 \
-e html tsv \
-o out.phg \
--delete-shorts \
-p \
--not-open ;
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[be/41a274] process > BACANNOT:KOFAMSCAN (sthermophilus) [ 0%] 0 of 1
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[02/cce239] process > BACANNOT:ISLANDPATH (sthermophilus) [100%] 1 of 1 ✔
[bf/fd24d1] process > BACANNOT:VFDB (sthermophilus) [100%] 1 of 1 ✔
[5c/906ff6] process > BACANNOT:VICTORS (sthermophilus) [100%] 1 of 1 ✔
[2b/d43309] process > BACANNOT:PHAST (sthermophilus) [100%] 1 of 1 ✔
[0e/a237fe] process > BACANNOT:PHIGARO (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[9c/9bab7a] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1 ✔
[41/a6274d] process > BACANNOT:ICEBERG (sthermophilus) [100%] 1 of 1 ✔
[f5/c6cb20] process > BACANNOT:AMRFINDER (sthermophilus) [100%] 1 of 1 ✔
[eb/0cfd15] process > BACANNOT:CARD_RGI (sthermophilus) [100%] 1 of 1 ✔
[16/30413d] process > BACANNOT:ARGMINER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[b6/12d966] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[d7/019954] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1 ✔
[47/c7d59b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1 ✔
[48/dfd034] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'BACANNOT:PHIGARO (sthermophilus)'
Caused by:
Process `BACANNOT:PHIGARO (sthermophilus)` terminated with an error exit status (1)
Command executed:
# activate env
source activate phigaro
# get tool version
phigaro -V > phigaro_version.txt ;
# create new config to properly load database
cp $(which config.yml) ./custom_config.yml ;
sed -i "s|CHANGE_PVOG|bacannot_dbs/phigaro_db/allpvoghmms|" ./custom_config.yml ;
HMM_BIN=$(which hmmsearch) ;
sed -i "s|CHANGE_HMMSEARCH|$HMM_BIN|" ./custom_config.yml ;
PRODIGAL_BIN=$(which prodigal) ;
sed -i "s|CHANGE_PRODIGAL|$PRODIGAL_BIN|" ./custom_config.yml ;
# run phigaro
phigaro \
-f assembly.fasta \
--config ./custom_config.yml \
-t 4 \
-e html tsv \
-o out.phg \
--delete-shorts \
-p \
--not-open ;
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[be/41a274] process > BACANNOT:KOFAMSCAN (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[02/cce239] process > BACANNOT:ISLANDPATH (sthermophilus) [100%] 1 of 1 ✔
[bf/fd24d1] process > BACANNOT:VFDB (sthermophilus) [100%] 1 of 1 ✔
[5c/906ff6] process > BACANNOT:VICTORS (sthermophilus) [100%] 1 of 1 ✔
[2b/d43309] process > BACANNOT:PHAST (sthermophilus) [100%] 1 of 1 ✔
[0e/a237fe] process > BACANNOT:PHIGARO (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[9c/9bab7a] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1 ✔
[41/a6274d] process > BACANNOT:ICEBERG (sthermophilus) [100%] 1 of 1 ✔
[f5/c6cb20] process > BACANNOT:AMRFINDER (sthermophilus) [100%] 1 of 1 ✔
[eb/0cfd15] process > BACANNOT:CARD_RGI (sthermophilus) [100%] 1 of 1 ✔
[16/30413d] process > BACANNOT:ARGMINER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[b6/12d966] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[d7/019954] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1 ✔
[47/c7d59b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1 ✔
[48/dfd034] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Error executing process > 'BACANNOT:PHIGARO (sthermophilus)'
Caused by:
Process `BACANNOT:PHIGARO (sthermophilus)` terminated with an error exit status (1)
Command executed:
# activate env
source activate phigaro
# get tool version
phigaro -V > phigaro_version.txt ;
# create new config to properly load database
cp $(which config.yml) ./custom_config.yml ;
sed -i "s|CHANGE_PVOG|bacannot_dbs/phigaro_db/allpvoghmms|" ./custom_config.yml ;
HMM_BIN=$(which hmmsearch) ;
sed -i "s|CHANGE_HMMSEARCH|$HMM_BIN|" ./custom_config.yml ;
PRODIGAL_BIN=$(which prodigal) ;
sed -i "s|CHANGE_PRODIGAL|$PRODIGAL_BIN|" ./custom_config.yml ;
# run phigaro
phigaro \
-f assembly.fasta \
--config ./custom_config.yml \
-t 4 \
-e html tsv \
-o out.phg \
--delete-shorts \
-p \
--not-open ;
executor > local (21)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[d5/b3e974] process > BACANNOT:PROKKA (sthermophilus) [100%] 1 of 1 ✔
[68/7db222] process > BACANNOT:MLST (sthermophilus) [100%] 1 of 1 ✔
[5f/ca2d14] process > BACANNOT:BARRNAP (sthermophilus) [100%] 1 of 1 ✔
[a2/bcea9e] process > BACANNOT:COMPUTE_GC (sthermophilus) [100%] 1 of 1 ✔
[be/41a274] process > BACANNOT:KOFAMSCAN (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:KEGG_DECODER -
[ec/d59055] process > BACANNOT:PLASMIDFINDER (sthermophilus) [100%] 1 of 1 ✔
[6e/ffa58c] process > BACANNOT:PLATON (sthermophilus) [100%] 1 of 1 ✔
[02/cce239] process > BACANNOT:ISLANDPATH (sthermophilus) [100%] 1 of 1 ✔
[bf/fd24d1] process > BACANNOT:VFDB (sthermophilus) [100%] 1 of 1 ✔
[5c/906ff6] process > BACANNOT:VICTORS (sthermophilus) [100%] 1 of 1 ✔
[2b/d43309] process > BACANNOT:PHAST (sthermophilus) [100%] 1 of 1 ✔
[0e/a237fe] process > BACANNOT:PHIGARO (sthermophilus) [100%] 1 of 1, failed: 1 ✘
[9c/9bab7a] process > BACANNOT:PHISPY (sthermophilus) [100%] 1 of 1 ✔
[41/a6274d] process > BACANNOT:ICEBERG (sthermophilus) [100%] 1 of 1 ✔
[f5/c6cb20] process > BACANNOT:AMRFINDER (sthermophilus) [100%] 1 of 1 ✔
[eb/0cfd15] process > BACANNOT:CARD_RGI (sthermophilus) [100%] 1 of 1 ✔
[16/30413d] process > BACANNOT:ARGMINER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[b6/12d966] process > BACANNOT:REFSEQ_MASHER (sthermophilus) [100%] 1 of 1 ✔
[d7/019954] process > BACANNOT:DIGIS (sthermophilus) [100%] 1 of 1 ✔
[47/c7d59b] process > BACANNOT:ANTISMASH (sthermophilus) [100%] 1 of 1 ✔
[48/dfd034] process > BACANNOT:SEQUENCESERVER (sthermophilus) [100%] 1 of 1 ✔
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
Error executing process > 'BACANNOT:PHIGARO (sthermophilus)'
Caused by:
Process `BACANNOT:PHIGARO (sthermophilus)` terminated with an error exit status (1)
Command executed:
# activate env
source activate phigaro
# get tool version
phigaro -V > phigaro_version.txt ;
# create new config to properly load database
cp $(which config.yml) ./custom_config.yml ;
sed -i "s|CHANGE_PVOG|bacannot_dbs/phigaro_db/allpvoghmms|" ./custom_config.yml ;
HMM_BIN=$(which hmmsearch) ;
sed -i "s|CHANGE_HMMSEARCH|$HMM_BIN|" ./custom_config.yml ;
PRODIGAL_BIN=$(which prodigal) ;
sed -i "s|CHANGE_PRODIGAL|$PRODIGAL_BIN|" ./custom_config.yml ;
# run phigaro
phigaro \
-f assembly.fasta \
--config ./custom_config.yml \
-t 4 \
-e html tsv \
-o out.phg \
--delete-shorts \
-p \
--not-open ;
# change names
[ ! -s out.phg/assembly.phigaro.tsv ] || mv out.phg/assembly.phigaro.tsv sthermophilus_phigaro.tsv ;
[ ! -s out.phg/assembly.phigaro.html ] || mv out.phg/assembly.phigaro.html sthermophilus_phigaro.html ;
# create BED
grep -v "taxonomy" sthermophilus_phigaro.tsv | awk 'BEGIN { FS = " "; OFS="\t" } { print $1,$2,$3 }' > sthermophilus_phigaro.bed
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Work dir:
/choppy/work/0e/a237fed568f78233fbde4a0325225d
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`Fety
fmalmeida
commented
2 years ago I have an idea of what it may be. I'll give it a try after work.
😄
fmalmeida
commented
2 years ago Hi @fetyj,
It turns out that was a simple fix. In phigaro.nf I was assuming that a file would always be available ... but its not the case when output is empty. So, I was ignoring this possibility.
Now with the new version I could run it successfully with your dataset.
Please, give it a go and let me know of the outcome.
Please make sure to update the docker images and the pipeline itself.
Also, about the problem with the shiny app server you mentioned, I was not able to replicate it. I could successfully use the server with your data.
Maybe you need to update the server docker image you have as well.
So I would ask you to try again, and if the problem persists, please open a new issue related to the shiny server alone. Let's leave this ticket here only being related to the workflow finishing properly.
fetyj
commented
2 years ago Hi @fmalmeida, Thank you for the fix, everything went just fine and also the shiny app server just needed to be update :smiley: Fety
fmalmeida
commented
2 years ago Super 🎉
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)
```bash 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: