Closed m3hdad closed 2 months ago
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.
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:
/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
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
-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.
Description of the bug
A couple of months ago we had a slack thread about how
NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_PYRODIGAL_FNA
gets confused with meta.id and gz file path if sample names are repeated along full path to fasta file.The topic is discussed here on slack. Fix: Changing sample names solves the problem.
The input file which resulted in this error was:
changing the input file to the following fixed the issue:
Command used and terminal output
No response
Relevant files
No response
System information
No response