Hello,
Is it possible to generate an identity score value between two sequences using Mauve? Or is there another software that can provide such value?
Thank you
•
written
by
marongiu.luigi
FastANI has been recommended by users here for this type of comparison (since you are mentioning Mauve you are likely referring to genomes): https://github.com/ParBLiSS/FastANI
Thank you, I used [skani][1] but it requires the build a model of several genomes together. Can I use it for only two genomes?
The nf-core/pairgenomealign pipeline, which I develop, reports a percent identity score for pairs of genome. In the current version (2.0.0) gaps are counted as mismatches but I plan to update it so that an alternative score ignoring gaps is also provided. The pipeline uses LAST as an aligner. If you run the last-train program directly or through the pipeline, you will also find an estimate of the percent similarity (ignoring gaps) in the trained parameter file that it outputs.
Thank you. I prepared the samplesheet.csv file as
HoVa25_chr1, chr1_out.fa
Query_1, Valg_chr1_ref.fa
Query_2, Valg_V25_chr1_Cns.fa
opened the terminal in the folder containing all the files and ran nextflow run nf-core/pairgenomealign --target ./target_genome_file.fa --input ./samplesheet.csv --outdir ./results -profile dockerbut I got the error:
ERROR ~ Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* --input (./samplesheet.csv): Validation of file failed:
-> Entry 1: Missing required field(s): sample, fasta
-> Entry 2: Missing required field(s): sample, fast
What is the correct syntax?
Thank you, I tried but this time I got:
ERROR ~ Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* --input (./samplesheet.csv): Validation of file failed:
-> Entry 1: Error for field 'fasta' (chr1_out.fa): the file or directory 'chr1_out.fa' does not exist (Fasta file for genomes must be provided, cannot contain spaces and must have extension `.fa`, `.fa.gz`, `.fna`, `.fna.gz`, `.fasta` or `.fasta.gz`)
I then created the file chr1_out.fa in the working folder but then I got:
[- ] NFC…AIRGENOMEALIGN:CUTN_TARGET -
[- ] NFC…PAIRGENOMEALIGN:CUTN_QUERY -
[- ] NFC…AIRGENOMEALIGN:CUTN_TARGET -
[- ] NFC…PAIRGENOMEALIGN:CUTN_QUERY -
[- ] NFC…IRGENOMEALIGN:ASSEMBLYSCAN -
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[- ] NFC…ALIGN_M2O:ALIGNMENT_LASTDB -
[- ] 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 ~ No such file or directory: /home/gigiux/Downloads/ALIGN/target_genome_file.fa
-- Check script '/home/gigiux/.nextflow/assets/nf-core/pairgenomealign/main.nf' at line: 83 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
-[nf-core/pairgenomealign] Pipeline completed with errors-
I created also target_genome_file.fa but now I got the error:
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB (target)'
Caused by:
Process requirement exceeds available CPUs -- req: 6; avail: 4
Command executed:
mkdir lastdb
lastdb \
-R01 -c -uYASS -S2 \
-P 6 \
lastdb/target \
target_genome_file.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:
-
Command output:
(empty)
Work dir:
/home/gigiux/Downloads/ALIGN/work/07/20c49e14a447e696f1bbf5c31dd86f
Container:
community.wave.seqera.io/library/last:1608--f41c047f7dc37e30
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- 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
Yes, you can make a nf.conf local file and include it with -c nf.conf, taking example on the following profile from the default configs:
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
https://github.com/nf-core/pairgenomealign/blob/2.0.0/nextflow.config#L172-L183
Or if this profile happens to fit your needs well, you can include with the -p option. You probably still need docker, so that would be -p docker,gitput. (not tested)
I finally got access to a more powerful machine, but this time I got the error:
$ ~/src/Nextflow/nextflow run nf-core/pairgenomealign ./target_genome_file.fa --input ./samplesheet.csv --outdir ./results -profile docker
N E X T F L O W ~ version 25.05.0-edge
Launching `https://github.com/nf-core/pairgenomealign` [thirsty_escher] DSL2 - revision: 0005fc64fc [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/pairgenomealign 2.2.0dev
------------------------------------------------------
Input/output options
input : ./samplesheet.csv
outdir : ./results
Alignment options
last_split_mismap : 1e-05
Generic options
trace_report_suffix: 2025-06-08_10-25-29
Core Nextflow options
revision : master
runName : thirsty_escher
containerEngine : docker
launchDir : /home/gigiux/Downloads/ALIGN
workDir : /home/gigiux/Downloads/ALIGN/work
projectDir : /home/gigiux/.nextflow/assets/nf-core/pairgenomealign
userName : gigiux
profile : docker
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
ERROR ~ Validation of pipeline parameters failed!
-- Check '.nextflow.log' file for details
The following invalid input values have been detected:
* Missing required parameter(s): target
-- Check script '/home/gigiux/.nextflow/assets/nf-core/pairgenomealign/subworkflows/nf-core/utils_nfschema_plugin/main.nf' at line: 39 or see '.nextflow.log' file for more details
What is the parameter target missing?
Thank you
Usage section for the pipeline: https://nf-co.re/pairgenomealign/2.1.0/docs/usage/
You need to specify a "target" genome using the parameter --target, which in your case is the target_genome_file.fa (or whatever the real name is).
Yes, there was the --target parameter missing. I tried again, this time with a samplesheet.csv file containing only
sample, fasta
Query_1, Valg_chr1_ref.fa
(I am essentially comparing Valg_V25_chr1_Cns.fa to Valg_chr1_ref.fa) but I got:
$ ~/src/Nextflow/nextflow run nf-core/pairgenomealign --target ./Valg_V25_chr1_Cns.fa --input ./samplesheet.csv --outdir ./results -profile docker
N E X T F L O W ~ version 25.05.0-edge
Launching `https://github.com/nf-core/pairgenomealign` [zen_goldberg] 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: 2025-06-09_07-02-32
Core Nextflow options
revision : master
runName : zen_goldberg
containerEngine : docker
launchDir : /home/gigiux/Downloads/ALIGN
workDir : /home/gigiux/Downloads/ALIGN/work
projectDir : /home/gigiux/.nextflow/assets/nf-core/pairgenomealign
userName : gigiux
profile : docker
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
executor > local (4)
[91/dc3644] NFC…CUTN_TARGET (targetGenome) | 0 of 1
[79/83afe9] NFC…ALIGN:CUTN_QUERY (Query_1) | 0 of 1 x
[36/98987c] NFC…IGN:ASSEMBLYSCAN (Query_1) | 0 of 1 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[6b/b049b8] 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 -
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)` terminated with an error exit status (127)
Command executed:
seqtk \
cutN \
-n 10 -p 100000 \
-g Valg_V25_chr1_Cns.fa \
> targetGenome.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET":
executor > local (4)
[91/dc3644] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[79/83afe9] NFC…ALIGN:CUTN_QUERY (Query_1) | 0 of 1 x
[36/98987c] NFC…IGN:ASSEMBLYSCAN (Query_1) | 0 of 1 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[6b/b049b8] 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:CUTN_TARGET (targetGenome)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)` terminated with an error exit status (127)
Command executed:
seqtk \
cutN \
-n 10 -p 100000 \
-g Valg_V25_chr1_Cns.fa \
> targetGenome.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET":
seqtk: $(echo $(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*$//')
END_VERSIONS
Command exit status:
executor > local (4)
[91/dc3644] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[79/83afe9] NFC…ALIGN:CUTN_QUERY (Query_1) | 0 of 1 x
[36/98987c] NFC…IGN:ASSEMBLYSCAN (Query_1) | 0 of 1 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[6b/b049b8] 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 | 0 of 1
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pairgenomealign] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)` terminated with an error exit status (127)
Command executed:
seqtk \
cutN \
-n 10 -p 100000 \
-g Valg_V25_chr1_Cns.fa \
> targetGenome.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET":
seqtk: $(echo $(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*$//')
END_VERSIONS
Command exit status:
executor > local (4)
[91/dc3644] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[79/83afe9] NFC…ALIGN:CUTN_QUERY (Query_1) | 0 of 1 x
[36/98987c] NFC…IGN:ASSEMBLYSCAN (Query_1) | 0 of 1 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[6b/b049b8] 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 | 0 of 1
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/pairgenomealign] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)'
Caused by:
Process `NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET (targetGenome)` terminated with an error exit status (127)
Command executed:
seqtk \
cutN \
-n 10 -p 100000 \
-g Valg_V25_chr1_Cns.fa \
> targetGenome.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:CUTN_TARGET":
seqtk: $(echo $(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*$//')
END_VERSIONS
Command exit status:
127
Command output:
(empty)
Command error:
.command.run: line 304: docker: command not found
Work dir:
/home/gigiux/Downloads/ALIGN/work/91/dc3644158a6a35e027a160fa96efcd
Container:
quay.io/biocontainers/seqtk:1.4--he4a0461_1
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
What went wrong this time? Thank you
.command.run: line 304: docker: command not found: You need either to install the software by yourself, or to let Nextflow download them for you using conda, docker or singularity. Here you specified -profile docker, and the pipeline tries to use it, however it appears to not be installed.
Hello again. I managed to install Nextflow on a more powerful machine but I got the following error:
$ nextflow run nf-core/pairgenomealign --target ./target_genome_file.fa --input ./samplesheet.csv --outdir ./results -profile docker
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 [f4e1715bf4]
Launching `https://github.com/nf-core/pairgenomealign` [pedantic_carlsson] DSL2 - revision: 0005fc64fc [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/pairgenomealign 2.2.0dev
------------------------------------------------------
Input/output options
input : ./samplesheet.csv
target : ./target_genome_file.fa
outdir : ./results
Alignment options
last_split_mismap : 1e-05
Generic options
trace_report_suffix: 2025-08-08_08-01-44
Core Nextflow options
revision : master
runName : pedantic_carlsson
containerEngine : docker
launchDir : /home/gigiux/Documents/ALIGN
workDir : /home/gigiux/Documents/ALIGN/work
projectDir : /home/gigiux/.nextflow/assets/nf-core/pairgenomealign
userName : gigiux
profile : docker
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
executor > local (6)
[e9/f52029] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[42/40beee] NFC…ALIGN:CUTN_QUERY (Query_2) | 0 of 3
[4f/9f5d12] NFC…IGN:ASSEMBLYSCAN (Query_2) | 0 of 3
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[f7/da7733] 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 \
target_genome_file.fa
cat <<-END_VERSIONS > versions.yml
"NFCORE_PAIRGENOMEALIGN:PAIRGENOMEALIGN:PAIRALIGN_M2O:ALIGNMENT_LASTDB":
executor > local (8)
[e9/f52029] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[1e/d3976d] NFC…N:CUTN_QUERY (HoVa25_chr1) | 0 of 3
[0f/1239aa] NFC…IGN:ASSEMBLYSCAN (Query_1) | 0 of 3
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[f7/da7733] 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 \
target_genome_file.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:
executor > local (8)
[e9/f52029] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[c7/7a552b] NFC…ALIGN:CUTN_QUERY (Query_1) | 0 of 3 x
[4f/9f5d12] NFC…IGN:ASSEMBLYSCAN (Query_2) | 0 of 3 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[f7/da7733] 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 \
target_genome_file.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:
executor > local (8)
[e9/f52029] NFC…CUTN_TARGET (targetGenome) | 0 of 1 x
[c7/7a552b] NFC…ALIGN:CUTN_QUERY (Query_1) | 0 of 3 x
[4f/9f5d12] NFC…IGN:ASSEMBLYSCAN (Query_2) | 0 of 3 x
[- ] NFC…IQC_ASSEMBLYSCAN_PLOT_DATA -
[f7/da7733] 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 \
target_genome_file.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.run: line 304: docker: command not found
Work dir:
/home/gigiux/Documents/ALIGN/work/f7/da77332adcf1a3f7b4d863d6e7a47b
Container:
community.wave.seqera.io/library/last:1611--e1193b3871fa0975
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
What would be the problem?
Thank you
Log in to answer this question.
According to the manual a file is supposed to be produced by Mauve: https://darlinglab.org/mauve/user-guide/files.html#:~:text=The%20identity%20matrix%20file,every%20homologous%20nucleotide%20was%20identical.
Thank you, I ran with
progressiveMauve --weight=15 --output=./out_file.mauve chr1.fawherechr1.fais a multifasta with the two genomes to align. The output isout_file.mauve, out_file.mauve.backbone, out_file.mauve.bbcolsbut they don't provide identity score. I think I am missing an argument...Perhaps the matrix generation requires more than two input genomes. Can you try providing one of the genomes two times in your input file?
I am not sure I can attach such a large file; would the ID of the genome be the same? NZ_CP184833.1 (https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP184833.1). Thank you
What I was thinking that you could duplicate one of the genomes in this file (and give it a dummy name) and then see if
mauveproduces a percent identity file (when there are 3 genomes in the file).I see, thanks I ran mauve with 3 files input and I got
out_file.mauve.bbcols, out_file.mauve, out_file.mauve.backbonebut none with the identity value...