jmwhitha commented 3 years ago

Good afternoon,

My script is giving me an error when I try to transfer some data into my working directory. I think something is wrong with prefetch.

Thank you for your help in advance,

###########################SCRIPT###############################

!/bin/tcsh

BSUB -n 1

BSUB -x

BSUB -W 600

BSUB -J mycode

BSUB -o stdout.%J

BSUB -e stderr.%J

conda activate /usr/local/usrapps/metagenomics/env_sra-tools

vdb-config --restore-defaults

open the SRR folder you want

these numbers are associated with samples saved at NCBI

SRR13355283 is for a Tibetan kefir grain metagenome

prefetch SRR13355283

retrieve the fastq file and leave the rest

I is for paired-end reads

fastq-dump-orig.2.11.0 -I SRR13355283

conda deactivate /usr/local/usrapps/metagenomics/env_sra-toolkit.csh

########################SCRIPT##############################

########################RESULT#############################

2021-07-14T17:22:34 fastq-dump-orig.2.11.0 err: item not found while constructing within virtual database module - the path 'SRR13355283' cannot be opened as database or table deactivate does not accept arguments remainder_args: ['/usr/local/usrapps/metagenomics/env_sra-toolkit.csh']

########################RESULT###################################

klymenko commented 2 years ago

We already had similar issues with conda. We don't support it. Use our build.

jmwhitha commented 2 years ago

Okay thank you :)

On Thu, Sep 30, 2021 at 2:52 PM Andrew Klymenko @.***> wrote:

We already had similar issues https://github.com/ncbi/sra-tools/issues/497 with conda. We don't support it. Use our build https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.

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