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2 days ago
marongiu.luigi
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I have isolated a genome from a bacterium and I would like to determine the percentage of identity with the reference genome. I understand that nf-core of NextFlow is a good tool for the job, but it did not work for me.
I installed NextFlow with conda create --name env_nf nextflow, I then activated NextFlow with conda activate env_nf, renamed it as conda create --name env_nf nextflow, and updated the tool with nextflow self-update.
I am working on a folder that contains these files:
$ ls
chr1_out.fa samplesheet.csv Valg_chr1_ref.fa Valg_V25_chr1_Cns.fa
$ cat samplesheet.csv
sample,fasta
HoVa25_chr1, chr1_out.fa
Query_1, Valg_chr1_ref.fa
Query_2, Valg_V25_chr1_Cns.fa
$ head Valg_chr1_ref.fa # reference file
>NZ_CP098033.1 Vibrio alginolyticus strain E110 chromosome 1, complete sequence
ATGATGAAAAGCCACCGTTTTACGCCCTTTGCTTTACCCTTGTGGTTAGTTATCTGTTTCGGTTTCCTCC
TGAGCAGTAGTGTGTTGGCTCAAGATATTCGTGACGTTCAACGAGAGCATGGTGTAGAGTTACTAGCGTG
GGTTGGTAAACAACCAACGGCTGGGGAGAAGCGTAAAACACCAAGTTTTAGCGTCAATGAGCAAGTTATT
TTAACCATCGAAGTGGCAACGCCGCGTTGGTTTACGGGTGGTACGAGAATTGGCAATATTGAAATACCCA
ATGTTATCGCCAAACAGCGTAATCAACTAGCAACCAACTTTACTGAGCAAAAAGAGGGACAAACTTGGTC
GCGTCAACGCTGGGAAGTGACTTTGTATCCACAAGCATCTGGTGATTTTGTGATTCCACCTGTCGCTGTG
GGCGTTCAGGTGTCGGCGCCGGATGGCGAGAAGGTGTCAGGCACACTTTATACGCAGCCGATTAAGTTCA
AAACTGTCTTGCCATCGGGATTGTTGAGCGGTGATACGCCTTGGTTTTCTGCAACGCACGTAGACGTAAA
ACAAGAGTGGGAAACCTCCACTGAGTCACTCAAAGTTGGGGATGCAATCACGCGTAAAATCACCATTTTG
$ head Valg_V25_chr1_Cns.fa # the file to measure
>Vibrio alginolyticus HoVa25 chromosome 1
ATGATGAAAAGCCACCGTTTTACGCACTTTGCTTTACCCTTGTGGTTAGTTATCTGTTTCGGCTTCCTCC
TGAGCAGTAGCGTGTTGGCTCAAGATATTCGTGACGTTCAACGAAAGCATGGAGTTGAGTTACAAGCGTG
GGTTGGTAAACAACCAATGGCTGGAGAGAAGAGGAAAACACCAAGTTTTAGCGTCAATGAGCAAGTTATT
TTAACCATCGAAGTGGCAACGCCGCGTTGGTTTACGGGTGGTACGAGAATTGGCAATATTGAAATACCCA
ATGTTATCGCCAAACAGCGTAATCAACTAGCAACCAACTTTACTGAGCAAAAAGAGGGGCAAACTTGGTC
GCGTCAACGCTGGGAAGTGACTTTGTATCCTCAAGCTTCTGGTGATTTTGTGATTCCACCTGTCGCAGTG
GGCGTTCAGGTGTCTGCGCCGGACGGCGAGAAGGTGTCAGGCACACTTTACACGCAGCCGATTAAGTTCA
AAACCGTCTTGCCATCGGGCCTGCTGAGTGGTGAGACACCTTGGTTTTCTGCAACAGATGTAGAGGTAAA
GCAAGAGTGGGATACCTCCACTGAGTCACTCAAAGTTGGGGATGCAATCACGCGTAAAATCACCATTTCG
I then ran the following:
$ nextflow run nf-core/pairgenomealign --target ./Valg_V25_chr1_Cns.fa --input ./samplesheet.csv --outdir ./results
but I got the error:
N E X T F L O W ~ version 25.04.6
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [86a011b850]
Launching `https://github.com/nf-core/pairgenomealign` [focused_kimura] DSL2 - revision: 0005fc64fc [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/pairgenomealign 2.2.0dev
------------------------------------------------------
Input/output options
input : ./samplesheet.csv
target : ./Valg_V25_chr1_Cns.fa
outdir : ./results
Alignment options
last_split_mismap : 1e-05
Generic options
trace_report_suffix: 2025-09-01_08-57-59
Core Nextflow options
revision : master
runName : focused_kimura
launchDir : /home/gigiux/Documents/ALIGN
workDir : /home/gigiux/Documents/ALIGN/work
projectDir : /home/gigiux/.nextflow/assets/nf-core/pairgenomealign
userName : gigiux
profile : standard
configFiles :
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/pairgenomealign/blob/master/CITATIONS.md
WARN: [nf-core/pairgenomealign] You are attempting to run the pipeline without any custom configuration!
This will be dependent on your local compute environment but can be achieved via one or more of the following:
(1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`
(2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`
(3) Using your own local custom config e.g. `-c /path/to/your/custom.config`
Please refer to the quick start section and usage docs for the pipeline.
executor > local (6)
[d6/e49457] NFC…CUTN_TARGET (targetGenome) | 0 of 1
[15/d28f01] NFC…N:CUTN_QUERY (HoVa25_chr1) | 0 of 3
[a8/e02015] NFC…ASSEMBLYSCAN (HoVa25_chr1) | 0 of 3
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[24/d8c9c2] NFC…:ALIGNMENT_LASTDB (target) | 0 of 1
[- ] NFC…RALIGN_M2O:ALIGNMENT_TRAIN -
[- ] NFC…N_M2O:ALIGNMENT_LASTAL_M2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_M2O -
[- ] NFC…GN_M2O:ALIGNMENT_SPLIT_O2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_O2O -
[- ] NFC…GN:PAIRGENOMEALIGN:MULTIQC -
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)` terminated with an error exit status (127)
Command executed:
mkdir lastdb
lastdb \
-R01 -c -uYASS -S2 \
-P 6 \
lastdb/target \
Valg_V25_chr1_Cns.fa
executor > local (7)
[d6/e49457] NFC…CUTN_TARGET (targetGenome) | 0 of 1
[15/d28f01] NFC…N:CUTN_QUERY (HoVa25_chr1) | 0 of 3
[a8/e02015] NFC…ASSEMBLYSCAN (HoVa25_chr1) | 0 of 3
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[24/d8c9c2] NFC…:ALIGNMENT_LASTDB (target) | 0 of 1 x
[- ] NFC…RALIGN_M2O:ALIGNMENT_TRAIN -
[- ] NFC…N_M2O:ALIGNMENT_LASTAL_M2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_M2O -
[- ] NFC…GN_M2O:ALIGNMENT_SPLIT_O2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_O2O -
[- ] NFC…GN:PAIRGENOMEALIGN:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)` terminated with an error exit status (127)
Command executed:
mkdir lastdb
lastdb \
-R01 -c -uYASS -S2 \
-P 6 \
lastdb/target \
Valg_V25_chr1_Cns.fa
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB":
last: $(lastdb --version 2>&1 | sed 's/lastdb //')
executor > local (7)
[d6/e49457] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[15/d28f01] NFC…N:CUTN_QUERY (HoVa25_chr1) | 0 of 3
[a4/d7ae35] NFC…IGN:ASSEMBLYSCAN (Query_2) | 0 of 3 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[24/d8c9c2] NFC…:ALIGNMENT_LASTDB (target) | 0 of 1 x
[- ] NFC…RALIGN_M2O:ALIGNMENT_TRAIN -
[- ] NFC…N_M2O:ALIGNMENT_LASTAL_M2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_M2O -
[- ] NFC…GN_M2O:ALIGNMENT_SPLIT_O2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_O2O -
[- ] NFC…GN:PAIRGENOMEALIGN:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pairgenomealign] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)` terminated with an error exit status (127)
Command executed:
mkdir lastdb
lastdb \
-R01 -c -uYASS -S2 \
-P 6 \
lastdb/target \
Valg_V25_chr1_Cns.fa
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB":
last: $(lastdb --version 2>&1 | sed 's/lastdb //')
executor > local (7)
[d6/e49457] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[15/d28f01] NFC…N:CUTN_QUERY (HoVa25_chr1) | 0 of 3
[a4/d7ae35] NFC…IGN:ASSEMBLYSCAN (Query_2) | 0 of 3 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[24/d8c9c2] NFC…:ALIGNMENT_LASTDB (target) | 0 of 1 x
[- ] NFC…RALIGN_M2O:ALIGNMENT_TRAIN -
[- ] NFC…N_M2O:ALIGNMENT_LASTAL_M2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_M2O -
[- ] NFC…GN_M2O:ALIGNMENT_SPLIT_O2O -
[- ] NFC…_M2O:ALIGNMENT_DOTPLOT_O2O -
[- ] NFC…GN:PAIRGENOMEALIGN:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pairgenomealign] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)` terminated with an error exit status (127)
Command executed:
mkdir lastdb
lastdb \
-R01 -c -uYASS -S2 \
-P 6 \
lastdb/target \
Valg_V25_chr1_Cns.fa
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB":
last: $(lastdb --version 2>&1 | sed 's/lastdb //')
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 4: lastdb: command not found
Work dir:
/home/gigiux/Documents/ALIGN/work/24/d8c9c21fabd71bd1fc40b442abf866
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
To note that if I add the option -profile docker I still get an error.
What is the proper syntax to run NextFlow's nf-core?
Thank you
It sounds to me like you want to make scrambled eggs, but you are stuck because the mixer needs fixing. No worries, you can scramble the eggs with a whisk or fork.
This is to say that you don't have to complicate your life by installing the
nf-corepipeline. There are simple programs that are meant specifically for your problem.https://github.com/ParBLiSS/FastANI
Thank you. I ran
$ fastANI -q Valg_V25_chr1_Cns.fa -r Valg_chr1_ref.fa -o HoVa25_chr1and I gotis it the same error , do you have docker installed ?
do you have any of those tools: conda, mamba, singularity, docket . I suggest install any of those tool and re-run with the correct
-profileargument.I have conda installed...
but as far as I can see you keep using -profile docker.
We cannot guess what you're doing.
Looks like you have been trying to make this pipeline work for 4 months based on the last thread we had worked through --> How to generate identiy score between aligned sequences with Mauve? .
You seem to be hitting the same error with different programs in the pipeline, over that time.
Yep, that is exactly it: I still did not understand where the error is. Beside, the other post was too populated to be understandable. What am I getting wrong? Thanks
This is all a waste of time if you don't take the time learning the very Nextflow basics. For example, using profile Docker without having Docker installed is like starting a car with the right key where the mechanic has previously removed the entire engine. It just a priori makes no sense, indicating that you're going blind. Please take a Nextflow course before going into production.
What Genomax said: You keep asking the same question , you tell us "it doesn't work", people suggested some fix but as far as I can see you provide no feedback about your installation: did you install docker|apptainer|concat|etc...