Open Gian77 opened 2 months ago
workdir should be where the trimmed read files go while tempdir is where the spades temporary files are written during assembly
the error message from spades is: "== Warning == output dir is not empty! Please, clean output directory before run."
so maybe you need to make sure the output directory is not still there? check on?
$project_dir/outputs/test_genome
Hello Jason,
Thank you for the email. I still get the same error after following your suggestions.
This is the error
== Warning == output dir is not empty! Please, clean output directory before run.
SPAdes genome assembler v3.15.5
Usage: spades.py [options] -o <output_dir>
spades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths: --restart-from last
This is how I included the output directories
AAFTF pipeline \
...
--tmpdir /mnt/scratch/benucci/aaftf_temporary/ \
--workdir $project_dir/filtered/ \
--out $project_dir/outputs/test_genome
and this is what I have int he directories
[benucci@dev-amd20 project_PleurotusMartina24]$ ll outputs/
total 2.1G
-rw-r----- 1 benucci ShadeLab 184 Apr 19 17:01 spades.list
-rw-r----- 1 benucci ShadeLab 544M Apr 19 17:01 test_genome_1P.fastq.gz
-rw-r----- 1 benucci ShadeLab 568M Apr 19 17:01 test_genome_2P.fastq.gz
-rw-r----- 1 benucci ShadeLab 497M Apr 19 17:12 test_genome_filtered_1.fastq.gz
-rw-r----- 1 benucci ShadeLab 525M Apr 19 17:12 test_genome_filtered_2.fastq.gz
-rw-r----- 1 benucci ShadeLab 74K Apr 19 17:11 test_genome.mito.fasta
[benucci@dev-amd20 project_PleurotusMartina24]$ ll filtered/
total 2.0M
-rw-r----- 1 benucci ShadeLab 1.8M Apr 19 17:11 contamdb.fa
-rw-r----- 1 benucci ShadeLab 1.9K Apr 19 17:11 GCF_000819615.1_ViralProj14015_genomic.fna.gz
-rw-r----- 1 benucci ShadeLab 1.7M Apr 19 17:11 UniVec
[benucci@dev-amd20 benucci]$ ll /mnt/scratch/benucci/aaftf_temporary/
total 0
It seems like is writing the filtered reads in the --out
instead in the --workdir
.
Thank you,
Gian
Is the outputs/test_dir there already. Is outputs already made
These are spades errors because a folder exists or possibly
Just leave workdir off k guess
I don’t use the pipeline function. I run steps individually so maybe you hit an untested parameter option?
Sent from Gmail Mobile @.*** Jason Stajich - UC Riverside http://lab.stajich.org
On Mon, Apr 22, 2024 at 8:57 AM Gian Nico @.***> wrote:
Hello Jason,
Thank you for the email. I still get the same error after following your suggestions.
This is the error
== Warning == output dir is not empty! Please, clean output directory before run.
SPAdes genome assembler v3.15.5
Usage: spades.py [options] -o
spades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths: --restart-from last This is how I included the output directories
AAFTF pipeline \ ... --tmpdir /mnt/scratch/benucci/aaftf_temporary/ \ --workdir $project_dir/filtered/ \ --out $project_dir/outputs/test_genome
and this is what I have int he directories
@.*** project_PleurotusMartina24]$ ll outputs/ total 2.1G -rw-r----- 1 benucci ShadeLab 184 Apr 19 17:01 spades.list -rw-r----- 1 benucci ShadeLab 544M Apr 19 17:01 test_genome_1P.fastq.gz -rw-r----- 1 benucci ShadeLab 568M Apr 19 17:01 test_genome_2P.fastq.gz -rw-r----- 1 benucci ShadeLab 497M Apr 19 17:12 test_genome_filtered_1.fastq.gz -rw-r----- 1 benucci ShadeLab 525M Apr 19 17:12 test_genome_filtered_2.fastq.gz -rw-r----- 1 benucci ShadeLab 74K Apr 19 17:11 test_genome.mito.fasta
@.*** project_PleurotusMartina24]$ ll filtered/ total 2.0M -rw-r----- 1 benucci ShadeLab 1.8M Apr 19 17:11 contamdb.fa -rw-r----- 1 benucci ShadeLab 1.9K Apr 19 17:11 GCF_000819615.1_ViralProj14015_genomic.fna.gz -rw-r----- 1 benucci ShadeLab 1.7M Apr 19 17:11 UniVec
@.*** benucci]$ ll /mnt/scratch/benucci/aaftf_temporary/ total 0
It seems like is writing the filtered reads in the --out instead in the --workdir. Thank you,
Gian
— Reply to this email directly, view it on GitHub https://github.com/stajichlab/AAFTF/issues/27#issuecomment-2070005755, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL5O2MV3LYGO2JP22ZBH3Y6UXOFAVCNFSM6AAAAABGN5OKGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZQGAYDKNZVGU . You are receiving this because you commented.Message ID: @.***>
Hello @hyphaltip
it seems now it is working just using these two parameters below:
--tmpdir /mnt/scratch/benucci/aaftf_temporary \
--out test_genome
Is running since 2 days, we'll see what I get... Thanks, Gian
Hello,
I am trying to run the AAFTF pipeline to assemble several Pleurotus genomes (testing it on 1 genome only) and I thought to run it as a pipeline at first. I am getting this error below. Spades seems to fail, but I cannot find any spades .log file anywhere. What do you think? I am running it in HPC that uses SLURM, please see the slurm output and the submitted sbatch file attached.
Additionally, 1) I am not totally sure the difference between these options (see
AAFTF piepieline -h
option below) :--tmpdir TMPDIR Assembler temporary dir
and -w WORKDIR, --workdir WORKDIR temp directory2) and how to pass parameters to spades using the
--assembler_args ASSEMBLER_ARGS Additional SPAdes/Megahit arguments` if it is possible, for example, different kmer sizes etc. Please let me know if you me to put these in a different issue ticket. Thanks much! Gianaaftf_piperun.zip