Wrap-up dev and release v3.3
#88
Comments
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Hello, |
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It is missing a white space after dev,
Should be -r dev -latest and not -r dev-latest
;)
…On Fri, 8 Sep 2023 at 17.27, josefdiaz ***@***.***> wrote:
Hello,
I have worked with my colleague @CarmenMartinezSeijas
<https://github.com/CarmenMartinezSeijas> and we have tried to run
dev-version and we try that command and we have the next message
./nextflow run fmalmeida/bacannot --input bacannot_samplesheet.yaml
--output Resultadosconejosdev --bacannot_db ./bacannot_db_2023 --max_memory
100.GB -profile docker -r dev-latest N E X T F L O W ~ version 23.04.3
Project fmalmeida/bacannotcontains uncommitted changes -- Cannot switch
to revision: dev-latest
Thanks
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We try right now and we get that |
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Probably because this branch was deleted.
Do this before running:
rm -rf ~/.nextflow/assets/fmalmeida/bacannot
Normally it is installed in the home dir, but if not, please correct the
above path.
…On Fri, 8 Sep 2023 at 17.33, josefdiaz ***@***.***> wrote:
We try right now and we get that
/nextflow run fmalmeida/bacannot --input bacannot_samplesheet.yaml
--output Resultadosconejosdev --bacannot_db ./bacannot_db_2023 --max_memory
100.GB -profile docker -r dev -latest
N E X T F L O W ~ version 23.04.3
Pulling fmalmeida/bacannot ...
fmalmeida/bacannot contains uncommitted changes -- cannot pull from
repository
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It seems to work now, We will leave it running and give you feedback on Monday. |
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Hello, ./nextflow run fmalmeida/bacannot --input bacannot_samplesheet.yaml --output Resultadosconejosdev --bacannot_db ./bacannot_db_2023 --max_memory 100.GB -profile docker -r dev -latest
N E X T F L O W ~ version 23.04.3
Pulling fmalmeida/bacannot ...
Already-up-to-date
Launching `https://github.com/fmalmeida/bacannot` [exotic_mestorf] DSL2 - revision: 1ed4a8e4c4 [dev]
------------------------------------------------------
fmalmeida/bacannot v3.3
------------------------------------------------------
Core Nextflow options
revision : dev
runName : exotic_mestorf
containerEngine: docker
launchDir : /home/jfrancisco
workDir : /home/jfrancisco/work
projectDir : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot
userName : jfrancisco
profile : docker
configFiles : /home/jfrancisco/.nextflow/assets/fmalmeida/bacannot/nextflow.config
Input/output options
input : bacannot_samplesheet.yaml
output : Resultadosconejosdev
bacannot_db : ./bacannot_db_2023
Max job request options
max_memory : 100.GB
!! 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
------------------------------------------------------
executor > local (7)
[- ] process > BACANNOT:UNICYCLER -
[- ] process > BACANNOT:FLYE -
[1f/61f49e] process > BACANNOT:PROKKA (sample_2445) [ 7%] 7 of 90, failed: 7
[- ] 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:MOBSUITE -
[- ] process > BACANNOT:ISLANDPATH -
[- ] process > BACANNOT:INTEGRON_FINDER -
[- ] process > BACANNOT:INTEGRON_FINDER_2GFF -
[- ] process > BACANNOT:VFDB -
[- ] process > BACANNOT:VICTORS -
[- ] process > BACANNOT:PHAST -
[- ] process > BACANNOT:PHIGARO -
[- ] process > BACANNOT:PHISPY -
[- ] process > BACANNOT:ICEBERG -
[- ] process > BACANNOT:AMRFINDER -
[- ] process > BACANNOT:CARD_RGI -
[- ] process > BACANNOT:ARGMINER -
[- ] process > BACANNOT:RESFINDER -
[- ] process > BACANNOT:CALL_METHYLATION -
[- ] process > BACANNOT:REFSEQ_MASHER -
[- ] process > BACANNOT:DIGIS -
[- ] process > BACANNOT:ANTISMASH -
[- ] process > BACANNOT:SEQUENCESERVER -
[- ] process > BACANNOT:MERGE_ANNOTATIONS -
[- ] process > BACANNOT:DRAW_GIS -
[- ] process > BACANNOT:GFF2GBK -
[- ] process > BACANNOT:CREATE_SQL -
[- ] process > BACANNOT:JBROWSE -
[- ] process > BACANNOT:REPORT -
[- ] process > BACANNOT:SUMMARY -
[- ] process > BACANNOT:MERGE_SUMMARIES -
[- ] process > BACANNOT:CIRCOS -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'BACANNOT:PROKKA (sample_2554)'
Caused by:
Missing output file(s) `annotation` expected by process `BACANNOT:PROKKA (sample_2554)`
Command executed:
#!/usr/bin/env bash
# save prokka version
prokka -v &> prokka_version.txt ;
# where are default prokka dbs?
dbs_dir=$(prokka --listdb 2>&1 >/dev/null | grep "databases in" | cut -f 4 -d ":" | tr -d " ") ;
# get hmms that shall be used
# PGAP contains TIGRFAM hmm models. When not skipping PGAP, TIGRFAM is not loaded.
cp -r $dbs_dir prokka_db
cp bacannot_db_2023/prokka_db/TIGRFAMs_15.0.hmm prokka_db/hmm
# hmmpress
( cd prokka_db/hmm/ ; for i in *.hmm ; do hmmpress -f $i ; done )
# clean headers char limit
awk '{ if ($0 ~ />/) print substr($0,1,21) ; else print $0 }' > cleaned_header.fasta
# run prokka
prokka \
--dbdir prokka_db \
\
--outdir annotation \
--cpus 4 \
--mincontiglen 200 \
--prefix sample_2554 \
--genus '' \
--species '' \
--strain "sample_2554" \
cleaned_header.fasta
# remove tmp dir to gain space
rm -r prokka_db
Command exit status:
0
Command output:
Working... done.
Pressed and indexed 1536 HMMs (1536 names).
Models pressed into binary file: HAMAP.hmm.h3m
SSI index for binary model file: HAMAP.hmm.h3i
Profiles (MSV part) pressed into: HAMAP.hmm.h3f
Profiles (remainder) pressed into: HAMAP.hmm.h3p
Working... done.
Pressed and indexed 4488 HMMs (4488 names and 4488 accessions).
Models pressed into binary file: TIGRFAMs_15.0.hmm.h3m
SSI index for binary model file: TIGRFAMs_15.0.hmm.h3i
Profiles (MSV part) pressed into: TIGRFAMs_15.0.hmm.h3f
Profiles (remainder) pressed into: TIGRFAMs_15.0.hmm.h3p
Command error:
[10:45:53] This is prokka 1.14.6
[10:45:53] Written by Torsten Seemann <[email protected]>
[10:45:53] Homepage is https://github.com/tseemann/prokka
[10:45:53] Local time is Mon Sep 11 10:45:53 2023
[10:45:53] You are not telling me who you are!
[10:45:53] Operating system is linux
[10:45:53] You have BioPerl 1.7.8
Argument "1.7.8" isn't numeric in numeric lt (<) at /usr/local/bin/prokka line 259.
[10:45:53] System has 12 cores.
[10:45:53] Will use maximum of 4 cores.
[10:45:53] Annotating as >>> Bacteria <<<
[10:45:53] 'cleaned_header.fasta' is not a readable non-empty FASTA file
Work dir:
/home/jfrancisco/work/f5/d75e1f5b0246d17396f7a91410b6e7
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
How can I solve that prokka´s problem ? |
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Hello hello @josefdiaz , The problem seems to be with the FASTA file ("'cleaned_header.fasta' is not a readable non-empty FASTA file") Can you check both the files:
The command line for it seems to be missing the input FASTA to be cleaned, see: # clean headers char limit
awk '{ if ($0 ~ />/) print substr($0,1,21) ; else print $0 }' > cleaned_header.fastaCan you check if the samplesheet is proper and it has access to all FASTA files? I am also launching a run with the testing profile right now to try it as I have to finalise the tests to make a release. Finally, since this is a testing run, just to make sure dev is proper for a release, I advise to not execute many samples with a testing/developing branch. Thus, I would be advising to execute it with only one to three samples. |
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My testing run is working fine. Maybe it is something with the samplesheet or input file. |
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You can also try it, just to check if it works, instead of using |
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#30 will stay out of release Last thing needed is updating the documentation |
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#93 merged |
Wrap up all the work in dev branch and release v3.3.
Needs:
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