Snakemake error with blast
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Entering edit mode
3 months ago
kamanovae ▴ 50

Hi!

I am trying to run the Blast with snakemake in different ways. Now the code looks like this:

rule blastn:
        input: nt=config["nt"], data1=config["out_LD"] + "contigs_coverage_more_10.fasta", data2=config["nt_folder"]
        output: output1=config["out_LD"] + "{sample}_noLD_spades_cov20.blast"
        shell: " blastn -query {input.data1} -db {input.data2}  -out {output.output1}"

I used to use a script that worked well, but now I need to rewrite it in snakemake

cd /storage1/db/ncbi/nt

    while read x
    do

    blastn -query /storage1/LD_proj/${x}/${x}_noLD_spades/contigs_coverage_more_20.fasta -db nt -out /storage1/LD_proj/${x}/${x}_noLD_spades_cov20.blast

    done<$1

The following error occurs:

BLAST Database error: No alias or index file found for nucleotide database [/storage1/db/ncbi/nt] in search path [/storage1/kaman/Ldec_all::]
[Thu Jul  8 13:05:38 2021]
Error in rule blastn:
    jobid: 34
    output: out_LD/SRR13510812_noLD_spades_cov20.blast
    shell:
         blastn -query out_LD/contigs_coverage_more_10.fasta -db /storage1/db/ncbi/nt  -out out_LD/SRR13510812_noLD_spades_cov20.blast
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

I can't correctly use the cd command in the program Snakemake

Blast cd Snakemake • 180 views
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Entering edit mode

You need to verify that the /storage1/db/ncbi/nt truly contains the database. In your script, the db is located at directory /storage1/starchevskaya/db/ncbi/nt.

You need to pass the path to the database in the format [PATH TO THE DB DIR]/[DB NAME] for your script, this would almost certainly look like /storage1/starchevskaya/db/ncbi/nt/nt

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