Wrap-up `dev` and release v3.3
fmalmeida opened this issue · 12 comments
Hello,
I have worked with my colleague @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
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
It seems to work now, We will leave it running and give you feedback on Monday.
Thank you so much
Hello,
I have tried to run the pipeline after the previous fixes and I 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 ...
Already-up-to-date
Launching `https://github.com/fmalmeida/bacannot` [exotic_mestorf] DSL2 - revision: 1ed4a8e4c4 [dev]
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fmalmeida/bacannot v3.3
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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 !!
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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
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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 <torsten.seemann@gmail.com>
[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 ?
Thanks
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:
/home/jfrancisco/work/f5/d75e1f5b0246d17396f7a91410b6e7/cleaned_header.fasta
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.
My testing run is working fine. Maybe it is something with the samplesheet or input file.
You can also try it, just to check if it works, instead of using --input you use -profile test,docker