spades assembly failed about aaftf HOT 4 OPEN

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 <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 $project_dir/outputs/test_genome and this is what I have int he directories ***@***.*** project_PleurotusMartina24]$ 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 <#27 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAL5O2MV3LYGO2JP22ZBH3Y6UXOFAVCNFSM6AAAAABGN5OKGOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZQGAYDKNZVGU> . You are receiving this because you commented.Message ID: ***@***.***>