kevinmenden / hybrid-assembly Goto Github PK
View Code? Open in Web Editor NEWPipeline for hybrid assembly using short and long reads.
License: MIT License
Pipeline for hybrid assembly using short and long reads.
License: MIT License
Hi,
I am relatively new to using nextflow. I get an error when I try to use canu assembler using the following command. May I know, how to resolve this error?
$ time nextflow run kevinmenden/hybrid-assembly --shortReads '/data01/nextflow_test/1_Raw_data/Illumina/N16005/*_L2_{1,2}.fq.gz' --longReads '/data01/nextflow_test/1_Raw_data/Nanopore/N16005_Nanopore.fastq' --assembler canu --genomeSize 2.8m -profile docker
N E X T F L O W ~ version 21.04.3
Launching `kevinmenden/hybrid-assembly` [nostalgic_wright] - revision: c2aef5f047 [master]
=========================================
hybrid-assembly v0.3.2dev
=========================================
WARN: Access to undefined parameter `max_memory` -- Initialise it to a default value eg. `params.max_memory = some_value`
WARN: Access to undefined parameter `max_cpus` -- Initialise it to a default value eg. `params.max_cpus = some_value`
WARN: Access to undefined parameter `max_time` -- Initialise it to a default value eg. `params.max_time = some_value`
Run Name : nostalgic_wright
Short Reads : /data01/nextflow_test/1_Raw_data/Illumina/N16005/*_L2_{1,2}.fq.gz
Long Reads : /data01/nextflow_test/1_Raw_data/Nanopore/N16005_Nanopore.fastq
Fasta Ref : false
Max Memory : null
Max CPUs : null
Max Time : null
Output dir : ./results
Working dir : /data01/nextflow_test/1_Raw_data/work
Container : kevinmenden/hybrid-assembly:latest
Pipeline Release: master
Current home : /home/prakki
Current user : prakki
Current path : /data01/nextflow_test/1_Raw_data
Script dir : /home/prakki/.nextflow/assets/kevinmenden/hybrid-assembly
Config Profile : docker
=========================================
executor > local (3)
[88/c0b23d] process > get_software_versions [ 0%] 0 of 1
[4c/49b783] process > fastqc (N16005_DDMS210004243-1a_HFMWLDSX2) [ 0%] 0 of 1
[25/884a7c] process > canu (N16005_Nanopore) [ 0%] 0 of 1
[- ] process > minimap -
[- ] process > pilon -
[- ] process > quast_canu -
[- ] process > multiqc -
Error executing process > 'canu (N16005_Nanopore)'
Caused by:
Process `canu (N16005_Nanopore)` terminated with an error exit status (1)
Command executed:
canu \
-p N16005_Nanopore genomeSize=2.8m -nanopore-raw N16005_Nanopore.fastq gnuplotTested=true \
correctedErrorRate=0.144 \
rawErrorRate=0.500 \
minReadLength=1000 \
minOverlapLength=500
Command exit status:
1
Command output:
usage: canu [-correct | -trim | -assemble | -trim-assemble] \
[-s <assembly-specifications-file>] \
-p <assembly-prefix> \
-d <assembly-directory> \
genomeSize=<number>[g|m|k] \
errorRate=0.X \
[other-options] \
[-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] *fastq
By default, all three stages (correct, trim, assemble) are computed.
To compute only a single stage, use:
-correct - generate corrected reads
-trim - generate trimmed reads
-assemble - generate an assembly
-trim-assemble - generate trimmed reads and then assemble them
The assembly is computed in the (created) -d <assembly-directory>, with most
files named using the -p <assembly-prefix>.
The genome size is your best guess of the genome size of what is being assembled.
It is used mostly to compute coverage in reads. Fractional values are allowed: '4.7m'
is the same as '4700k' and '4700000'
The errorRate is not used correctly (we're working on it). Don't set it
If you want to change the defaults, use the various utg*ErrorRate options.
A full list of options can be printed with '-options'. All options
can be supplied in an optional sepc file.
Reads can be either FASTA or FASTQ format, uncompressed, or compressed
with gz, bz2 or xz. Reads are specified by the technology they were
generated with:
-pacbio-raw <files>
-pacbio-corrected <files>
-nanopore-raw <files>
-nanopore-corrected <files>
Complete documentation at http://canu.readthedocs.org/en/latest/
ERROR: Directory not supplied with -d.
ERROR: Paramter 'correctedErrorRate' is not known.
ERROR: Paramter 'rawErrorRate' is not known.
executor > local (3)
[- ] process > get_software_versions -
[- ] process > fastqc (N16005_DDMS210004243-1a_HFMWLDSX2) -
[25/884a7c] process > canu (N16005_Nanopore) [100%] 1 of 1, failed: 1 ✘
[- ] process > minimap -
[- ] process > pilon -
[- ] process > quast_canu -
[- ] process > multiqc -
Error executing process > 'canu (N16005_Nanopore)'
Caused by:
Process `canu (N16005_Nanopore)` terminated with an error exit status (1)
Command executed:
canu \
-p N16005_Nanopore genomeSize=2.8m -nanopore-raw N16005_Nanopore.fastq gnuplotTested=true \
correctedErrorRate=0.144 \
rawErrorRate=0.500 \
minReadLength=1000 \
minOverlapLength=500
Command exit status:
1
Command output:
usage: canu [-correct | -trim | -assemble | -trim-assemble] \
[-s <assembly-specifications-file>] \
-p <assembly-prefix> \
-d <assembly-directory> \
genomeSize=<number>[g|m|k] \
errorRate=0.X \
[other-options] \
[-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] *fastq
By default, all three stages (correct, trim, assemble) are computed.
To compute only a single stage, use:
-correct - generate corrected reads
-trim - generate trimmed reads
-assemble - generate an assembly
-trim-assemble - generate trimmed reads and then assemble them
The assembly is computed in the (created) -d <assembly-directory>, with most
files named using the -p <assembly-prefix>.
The genome size is your best guess of the genome size of what is being assembled.
It is used mostly to compute coverage in reads. Fractional values are allowed: '4.7m'
is the same as '4700k' and '4700000'
The errorRate is not used correctly (we're working on it). Don't set it
If you want to change the defaults, use the various utg*ErrorRate options.
A full list of options can be printed with '-options'. All options
can be supplied in an optional sepc file.
Reads can be either FASTA or FASTQ format, uncompressed, or compressed
with gz, bz2 or xz. Reads are specified by the technology they were
generated with:
-pacbio-raw <files>
-pacbio-corrected <files>
-nanopore-raw <files>
-nanopore-corrected <files>
Complete documentation at http://canu.readthedocs.org/en/latest/
ERROR: Directory not supplied with -d.
ERROR: Paramter 'correctedErrorRate' is not known.
ERROR: Paramter 'rawErrorRate' is not known.
Command wrapper:
usage: canu [-correct | -trim | -assemble | -trim-assemble] \
[-s <assembly-specifications-file>] \
-p <assembly-prefix> \
-d <assembly-directory> \
genomeSize=<number>[g|m|k] \
errorRate=0.X \
[other-options] \
[-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] *fastq
By default, all three stages (correct, trim, assemble) are computed.
To compute only a single stage, use:
-correct - generate corrected reads
-trim - generate trimmed reads
-assemble - generate an assembly
-trim-assemble - generate trimmed reads and then assemble them
The assembly is computed in the (created) -d <assembly-directory>, with most
files named using the -p <assembly-prefix>.
The genome size is your best guess of the genome size of what is being assembled.
It is used mostly to compute coverage in reads. Fractional values are allowed: '4.7m'
is the same as '4700k' and '4700000'
The errorRate is not used correctly (we're working on it). Don't set it
If you want to change the defaults, use the various utg*ErrorRate options.
A full list of options can be printed with '-options'. All options
can be supplied in an optional sepc file.
Reads can be either FASTA or FASTQ format, uncompressed, or compressed
with gz, bz2 or xz. Reads are specified by the technology they were
generated with:
-pacbio-raw <files>
-pacbio-corrected <files>
-nanopore-raw <files>
-nanopore-corrected <files>
Complete documentation at http://canu.readthedocs.org/en/latest/
ERROR: Directory not supplied with -d.
ERROR: Paramter 'correctedErrorRate' is not known.
ERROR: Paramter 'rawErrorRate' is not known.
Work dir:
/data01/nextflow_test/1_Raw_data/work/25/884a7c241f4f68374c5fc59fcf6d14
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`
Dear Kevin,
I have run hybrid assembly with docker by following commands but it ended with an error.
Could you help me to find out is it memory error or something else.
(base) ThinkStation-P910:/data$ nextflow run kevinmenden/hybrid-assembly -profile docker --shortReads '*_R{1,2}.fastq.gz' --longReads combinedall.fastq --assembler spades
executor > local (3)
[8e/a9bc99] process > get_software_versions [100%] 1 of 1 ✔
[0e/54207c] process > fastqc (Q) [100%] 1 of 1 ✔
[5a/190f77] process > spades (Q) [ 0%] 0 of 1
[- ] process > quast_spades -
[- ] process > multiqc -
Error executing process > 'spades (Q)'
Caused by:
Process spades (Q)
terminated with an error exit status (1)
Command executed:
spades.py -o "spades_results" -t 16
-m 700
-1 Q_R1.fastq.gz -2 Q_R2.fastq.gz
--nanopore combinedall.fastq
-k 21,33,55,77
mv spades_results/scaffolds.fasta scaffolds.fasta
mv spades_results/contigs.fasta contigs.fasta
Command exit status:
1
.
.
.
.
.
== Error == system call for: "['/opt/conda/envs/assembly-env/share/spades-3.12.0-1/bin/spades-hammer', 'spades_results/corrected/configs/config.info']" finished abnormally, err code: -9
In case you have troubles running SPAdes, you can write to [email protected]
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
Work dir:
/media/laptop/zygopyllumtest/Q1 data/work/5a/190f77d2679c458bba66b2142565a1
Tip: when you have fixed the problem you can continue the execution adding the option -resume
to the run command line
I tried to use docker version but it shows the following error. Could you kindly help me to solve this.
Thank you
nextflow run kevinmenden/hybrid-assembly -profile docker --reads '/media/laptop/DBG2OLC-master/Pacbio.fasta'
N E X T F L O W ~ version 20.10.0
Launching kevinmenden/hybrid-assembly
[exotic_leakey] - revision: c2aef5f [master]
Path string cannot be empty
Missing fromPath
parameter
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