Comments (5)
Javaria-Ashraf
commented on August 22, 2024
Dear Ivan,
i think i have figured out the issue,
I found that the shovill version that the script installed by default is 0.9.0 in which there is no --assember option available, where as in newer version :
shovill
Synopsis:
Faster de novo assembly pipeline based around Spades
Usage:
shovill [options] --outdir DIR --R1 R1.fq.gz --R2 R2.fq.gz
Author:
Torsten Seemann <[email protected]>
Options:
--help This help
--version Print version and exit
--check Check dependencies are installed
--debug Debug info (default: OFF)
--cpus N Number of CPUs to use (default: 16)
--outdir XXX Output folder (default: '')
--namefmt XXX Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')
--force Force overwite of existing output folder (default: OFF)
--R1 XXX Read 1 FASTQ (default: '')
--R2 XXX Read 2 FASTQ (default: '')
--depth N Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)
--gsize XXX Estimated genome size <blank=AUTODETECT> (default: '')
--kmers XXX K-mers to use <blank=AUTO> (default: '')
--opts XXX Extra SPAdes options eg. --plasmid --sc ... (default: '')
--nocorr Disable post-assembly correction (default: OFF)
--trim Use Trimmomatic to remove common adaptors first (default: OFF)
--trimopt XXX Trimmomatic options (default: 'ILLUMINACLIP:/home/isd/miniconda3/envs/rMAP-1.0/bin/../db/trimmomatic.fa:1:30:11 LEADING:3 TRAILING:3 MINLEN:30 TOPHRED33')
--minlen N Minimum contig length <0=AUTO> (default: 1)
--mincov n.nn Minimum contig coverage <0=AUTO> (default: 2)
--asm XXX Spades result to correct: before_rr contigs scaffolds (default: 'contigs')
--tmpdir XXX Fast temporary directory (default: '/tmp')
--ram n.nn Try to keep RAM usage below this many GB (default: 8)
--keepfiles Keep intermediate files (default: OFF)
$ shovill --version
shovill 0.9.0
Whereas the newer version synopsis shown on the github readme shows the --assembler.
How do i fix this?
Thanks
Jia
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GunzIvan28
commented on August 22, 2024
Hey Asharaf,
I during my troubleshooting for the error you encountered, I tried a stand-alone run of the shovill software after removal of the --assembler option from my code and realized the program keeps blowing up because some perl modules can't be properly loaded. The snippet below shows the new errors that are coming up. I think Torsten the author changed something in the code....
$ shovill --R1 dataset-profile/trimmed_reads/ID246.clean_1.fastq.gz --R2 dataset-profile/trimmed_reads/ID246.clean_2.fastq.gz --cpus 12 --gsize 3.4M --force --outdir dataset-profile/assembly/ID246
Hello ivan
You ran: /home/ivan/miniconda3/envs/rMAP-1.0/bin/shovill --R1 dataset-profile/trimmed_reads/ID246.clean_1.fastq.gz --R2 dataset-profile/trimmed_reads/ID246.clean_2.fastq.gz --cpus 12 --gsize 3.4M --force --outdir dataset-profile/assembly/ID246
This is shovill 0.9.0
Written by Torsten Seemann <[email protected]>
Homepage is https://github.com/tseemann/shovill
Operating system is linux
Using seqtk - /home/ivan/miniconda3/envs/rMAP-1.0/bin/seqtk
Using pigz - /home/ivan/miniconda3/envs/rMAP-1.0/bin/pigz
Using kmc - /home/ivan/miniconda3/envs/rMAP-1.0/bin/kmc
Using trimmomatic - /home/ivan/miniconda3/envs/rMAP-1.0/bin/trimmomatic
Using lighter - /home/ivan/miniconda3/envs/rMAP-1.0/bin/lighter
Using flash - /home/ivan/miniconda3/envs/rMAP-1.0/bin/flash
Using spades.py - /home/ivan/miniconda3/envs/rMAP-1.0/bin/spades.py
Using bwa - /home/ivan/miniconda3/envs/rMAP-1.0/bin/bwa
Using samtools - /home/ivan/miniconda3/envs/rMAP-1.0/bin/samtools
Using java - /home/ivan/miniconda3/envs/rMAP-1.0/bin/java
Using pilon - /home/ivan/miniconda3/envs/rMAP-1.0/bin/pilon
Using tee - /home/ivan/miniconda3/envs/rMAP-1.0/bin/tee
Using vmstat - /usr/bin/vmstat
Error: /proc must be mounted
To mount /proc at boot you need an /etc/fstab line like:
proc /proc proc defaults
In the meantime, run "mount proc /proc -t proc"
Could not determine available RAM
So as I try to find a fix, use the megahit assembler for the time being since I tested it and rMAP runs pretty fine. When i find that fix for shovill, I will update the issue so let's keep this open for now.
Thanks
Ivan
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safinaARK
commented on August 22, 2024
Dear @GunzIvan28
There are two issues; one is the assembler shovill issue second is snpEFF:
by default when rMAP is installed via conda, it installs shovill version0.9.0 and that version does not have --assembler option so the quick fix is to edit the script by removing the --assembler option. Another is the script has a different version of sneff that is 4.5covid19-1 whereas by default conda install v 5.0 so again by changing the name in the rMAP script these issues will be solved.
@Javaria-Ashraf please do these changes, I hope it works for you too as it worked for me too.
thanks
SAR
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GunzIvan28
commented on August 22, 2024
@safinaARK,
I commend and salute you for taking the time to understand this pipeline like we the authors. Version 1 of rMAP was compiled during the COVID-19 pandemic and snpeff 4.5covid-19 what was available. Now depending on whether you are using a Mac or Ubuntu, the versions for snpeff both in the installers and the main script will have to change. I changed the version for the linux installer script to 5.0 because packages kept conflicting. I however haven't effected this change for the macos installer and the main script (both still use snpeff 4.5covid-19).
So @Javaria-Ashraf either you do as @safinaARK has directed or I can walk you through whatever changes you may have to make (again based on your system) whenever you find some time. All these changes will be amended in version 2 which we will release soon.
Lastly, @safinaARK I think you would be a good addition to the rMAP development. We are currently developing version 2 which we are implementing in the nextflow platform. If you are interested, I could add you as a collaborator. Just let me know.
Ivan
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safinaARK
commented on August 22, 2024
Thank you Ivan for the offer
Thanks once again for your acknowledgement
Reagrds
SAR
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Related Issues (11)
- Setup. Sh HOT 1
- Error on step: rMAP is will now perform Variant Calling HOT 4
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