Comments (2)
jfy133
commented on September 17, 2024
Looking again, Im' even more confused. I think the issue is coming further upstream, but I'm not sure where at the moment.
I have a suspion there is a faulty join function that is somehow merging the original FASTAs with some processed onat asome point. Then all downstream modules are for some reason get recieving both FASTAs rather than one.
That said, why cahnging the name would affect that I have no idea.
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jfy133
commented on September 17, 2024
I just tried replicating the issue and I am unable to.
Unfortuantely the slack thread doesn't have the command you used, but to describe what I just tested:
- Downloaded the assemblies (manually from ENA due to laziness), and placed in this structure
/home/james/git/nf-core/funcscan/testing/temp_inputs/GCA_000184535.1/GCA_000184535.1_ASM18453v1_genomic.fna
/home/james/git/nf-core/funcscan/testing/temp_inputs/GCA_000260455.1/GCA_000260455.1_ASM26045v1_genomic.fna
/home/james/git/nf-core/funcscan/testing/temp_inputs/GCA_000615725.1/GCA_000615725.1_ASM61572v1_genomic.fna- Created the following samplesheet
sample,fasta
GCA_000184535.1,/home/james/git/nf-core/funcscan/testing/temp_inputs/GCA_000184535.1/GCA_000184535.1_ASM18453v1_genomic.fna
GCA_000260455.1,/home/james/git/nf-core/funcscan/testing/temp_inputs/GCA_000260455.1/GCA_000260455.1_ASM26045v1_genomic.fna
GCA_000615725.1,/home/james/git/nf-core/funcscan/testing/temp_inputs/GCA_000615725.1/GCA_000615725.1_ASM61572v1_genomic.fna
- Ran the following command (on my local clone, with latest
-r dev) to completion with no error
$ nextflow run ../main.nf -profile docker --outdir ./results --input gunzip-confused-bug.csv --run_amp_screening --amp_skip_amplify --amp_skip_hmmsearch --run_arg_screening false
N E X T F L O W ~ version 24.04.2
Launching `../main.nf` [jolly_leavitt] DSL2 - revision: 70185db88e
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/funcscan v1.2.0dev
------------------------------------------------------
Core Nextflow options
runName : jolly_leavitt
containerEngine : docker
launchDir : /home/james/git/nf-core/funcscan/testing
workDir : /home/james/git/nf-core/funcscan/testing/work
projectDir : /home/james/git/nf-core/funcscan
userName : james
profile : docker
configFiles :
Input/output options
input : gunzip-confused-bug.csv
outdir : ./results
Screening Type Activation
run_amp_screening : true
AMP: AMPlify
amp_skip_amplify : true
AMP: HMMSearch
amp_skip_hmmsearch : true
AMP: ampcombi2 parsetables
amp_ampcombi_parsetables_dbevalue: 5
AMP: ampcombi2 cluster
amp_ampcombi_cluster_covmode : 0
amp_ampcombi_cluster_mode : 1
ARG: AMRFinderPlus
arg_amrfinderplus_identmin : -1
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/funcscan for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.7643099
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/funcscan/blob/master/CITATIONS.md
------------------------------------------------------
executor > local (31)
[- ] process > NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP -
[4f/1887d7] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:PYRODIGAL (GCA_000184535.1) [100%] 3 of 3 ✔
[b9/0695e8] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FAA (GCA_000184535.1_pyrodigal.faa.gz) [100%] 3 of 3 ✔
[4a/cf8818] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_FNA (GCA_000184535.1_pyrodigal.fna.gz) [100%] 3 of 3 ✔
[a4/b01a85] process > NFCORE_FUNCSCAN:FUNCSCAN:ANNOTATION:GUNZIP_PYRODIGAL_GBK (GCA_000184535.1_pyrodigal.gbk.gz) [100%] 3 of 3 ✔
[d8/1a619d] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:MACREL_CONTIGS (GCA_000184535.1) [100%] 3 of 3 ✔
[47/4e6a4a] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_PRED (GCA_000184535.1.macrel.prediction.gz) [100%] 3 of 3 ✔
[8f/8e6452] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:GUNZIP_MACREL_ORFS (GCA_000184535.1.macrel.all_orfs.faa.gz) [100%] 3 of 3 ✔
[11/acb89c] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPIR (GCA_000184535.1) [100%] 3 of 3 ✔
[b9/5d5743] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:DRAMP_DOWNLOAD [100%] 1 of 1 ✔
[d7/95481b] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_PARSETABLES (GCA_000615725.1) [100%] 3 of 3 ✔
[44/3f59b0] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_COMPLETE (ampcombi2) [100%] 1 of 1 ✔
[32/1cd22f] process > NFCORE_FUNCSCAN:FUNCSCAN:AMP:AMPCOMBI2_CLUSTER (ampcombi2) [100%] 1 of 1 ✔
[e4/aced66] process > NFCORE_FUNCSCAN:FUNCSCAN:MULTIQC [100%] 1 of 1 ✔
-[nf-core/funcscan] Pipeline completed successfully-Given we've overhauled the pipeline in a few places in how data is generated and sent around in -r dev, I'm guessing we have inadvertently fixed this issue as a side effect.
Therefore I'm going to close this for now, but if it crops up again when running the -r dev branch or on the next release, feel free to reopen.
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Related Issues (20)
- Remove warning about broken DeepBGC database links from docs HOT 1
- Add missing essential parameters for antismash HOT 4
- Fix BAKTA publish dir HOT 1
- Split input assemblies into BGC vs ARG/AMP compatible length types HOT 1
- Workflow diagram is broken in `dev` HOT 1
- deeparg 1.0.4 required to correctly fetch DBs HOT 1
- AMPLIFY_PREDICT exits with a ValueError while checking input HOT 1
- In some cases RGI will not produce all files expected for mving for publishing HOT 5
- The spliting of contigs into _long and _short should only be performed when needed, or at least it should be skippable HOT 1
- Missing abricate database download instructions in usage
- Missing icons for BGC sections in nextflow schema/parameter docs
- improving tool documentation & adding tests HOT 1
- A uniform input for all tools in each screening workflow HOT 2
- Missing Annotation files HOT 2
- Antismash parameter bug HOT 1
- Consider allowing annotation to run even if downstream screening not run
- A special samplesheet can delete all my sequences HOT 3
- nf-test wishlist
- comBGC column BGC_length inaccurate HOT 3
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