User: a.mostafa5050

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Posts by a.mostafa5050

<prev • 15 results • page 1 of 2 • next >
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Error in Blast+
... Hi everyone, I downloaded the nr database from NCBI in order to run Blast on Linux. I got the error message > "Error: mdb_env_open: No such file or directory" My slurm script is blastp -query /cluster/work/users/ahmedbar/prokka_result_AC/$SAMPLE_ID_1 -db /cluster/work/users/ahmedbar ...
alignment sequence written 5 weeks ago by a.mostafa50500
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Comment: C: Prokka error message
... But the database is found and I got this message before the error message `Looking for 'makeblastdb' - found /cluster/software/prokka/1.13.4-foss-2018b/bin/../binaries/linux/makeblastdb` ...
written 11 weeks ago by a.mostafa50500
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Comment: A: Prokka error message
... when I removed the `--setupdb`, the following error message appeared The sequence databases have not been indexed. Please run 'prokka --setupdb' first after that, I changed my script to prokka --setupdb --kingdom Bacteria -o $OUTPUTFILE.txt o- $OUTPUTFILE.tsv o- $OUTPUTFILE.tbl o- $OUTP ...
written 11 weeks ago by a.mostafa50500
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Comment: C: Novel protein identification
... Thanks a bundle, :) :) ...
written 12 weeks ago by a.mostafa50500
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Comment: C: Novel protein identification
... Do you mean searching in different databases such as NCBI and Uniprot to search for the function of the predicted protein?? ...
written 12 weeks ago by a.mostafa50500
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Novel protein identification
... Hi everybody, I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database. The question is how can I know that one of the predicted AR protein is a NOVEL?? Thanks ...
alignment written 12 weeks ago by a.mostafa50500 • updated 12 weeks ago by Qiongyi100
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Comment: C: HMMER software error message
... Yes, `HMMER_R` is a folder and I want the output files to be in it. so, which file should i add next to `--tblout` ...
written 3 months ago by a.mostafa50500
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Comment: C: HMMER software error message
... Thanks Fatima for helping. Really appreciate that. It worked, but I got another error message. > Failed to open tabular per-seq output file /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R for writing. ...
written 3 months ago by a.mostafa50500
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Comment: C: HMMER software error message
... sorry for the bad formatting in the previous two posts. I really appreciate your quick response. I tried the command you gave me, but still, the same error message appears. I would like to annotate protein sequences using the Resfams database. ...
written 3 months ago by a.mostafa50500
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Comment: C: HMMER software error message
... > I removed the back-slash and still gives me the same error message! > > this is the new script #!/bin/sh #SBATCH --job-name=HMMER_ahmed #SBATCH --account=nn9787k #SBATCH --time=08:30:00 #SBATCH --mem-per-cpu=4G #SBATCH --output=slurm-%j.base ## Set up jo ...
written 3 months ago by a.mostafa50500

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