bash submission

[Ahmad-40]

Hi, It works well on terminal like iseq -i CRR1117678 -p 10. But when we submit in the form of a bash script it gives an error.

!/bin/bash

SBATCH --job-name=test_download

SBATCH --partition=low,big,amd

SBATCH --nodes=1

SBATCH --ntasks-per-node=1

SBATCH --error=%j.err

SBATCH --output=%j.out

iseq -i CRR1117678 iseq -i CRR1117679

Error Error: CRR1117678 is not a valid Run accession. Error: CRR1117679 is not a valid Run accession.

[BioOmics]

Hi,

It's likely that your Slurm cluster is unable to access the network. You can try the following code to test if the network is working properly.

#!/bin/bash
#SBATCH --job-name=test_download
#SBATCH --partition=low,big,amd
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --error=%j.err
#SBATCH --output=%j.out

wget "https://ngdc.cncb.ac.cn/gsa/search?searchTerm=CRR1117678"

If you still have issues after testing, feel free to ask again.

[Ahmad-40]

I am also facing the following issue when using Aspera. What will be the Key passphrase: and password? iseq -i CRR1117499 -a -g Note: CRR1117499.metadata.csv exists, skip downloading metadata for CRR1117499 CRR1117499_f1.fq.gz 1.36G CRR1117499_r2.fq.gz 1.45G Note: Above Run will be downloaded. You can see the details in CRR1117499.metadata.csv File size: Database: GSA Mode: Aspera Key passphrase:

On Sat, Oct 26, 2024 at 9:25 PM BioOmics @.***> wrote:

Hi,

It's likely that your Slurm cluster is unable to access the network. You can try the following code to test if the network is working properly.

!/bin/bash#SBATCH --job-name=test_download#SBATCH --partition=low,big,amd#SBATCH --nodes=1#SBATCH --ntasks-per-node=1#SBATCH --error=%j.err#SBATCH --output=%j.out

wget https://ngdc.cncb.ac.cn/gsa/search?searchTerm=CRR1117678

If you still have issues after testing, feel free to ask again.

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-- Regards,

Dr. Bilal Ahmad +92-345-3800040

[BioOmics]

Please try:

wget "https://ngdc.cncb.ac.cn/gsa/file/downFile?fileName=download/aspera01.openssh" -O aspera01.openssh
ascp -P 33001 -i aspera01.openssh -QT -l 1000m -k1 -d aspera01@download.cncb.ac.cn:gsa2/CRA016056/CRR1117499/CRR1117499_f1.fq.gz .

Can the above code run normally? If so, iSeq should also run normally. Otherwise, you need to check your network or firewall or the key from GSA (aspera01.openssh)

[BioOmics]

If you have any other issues, feel free to reopen this issue at any time.