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Issue tracker for the Biostar Handbook
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Errors in fastq-dump and fastq-dump -X 1 -Z SRR1553591 #322

Open babasaraki opened 5 months ago

babasaraki commented 5 months ago

Have successfully installed all the software and then run $ ~/bin/doctor.py

Below is the output `$ ~/bin/doctor.py

Doctor! Doctor! Give me the news.

Checking symptoms ...

bwa ... OK

datamash ... OK

fastqc -h ... OK

hisat2 ... OK

seqret -h ... OK

featureCounts ... OK

efetch ... OK

esearch ... OK

samtools ... OK

fastq-dump --> ERROR

bowtie2 ... OK

bcftools ... OK

seqtk ... OK

seqkit ... OK

bio ... OK

fastq-dump -X 1 -Z SRR1553591 --> ERROR

#

Found some problems

#

Unable to run: fastq-dump, fastq-dump -X 1 -Z SRR1553591

#

Check the Biostar Handbook for installation help.

# (bioinfo)`

I followed all the necessary steps to solve this errors but still not working as expected.

Thank you for the support.

babasaraki commented 5 months ago

I used conda install -c bioconda sra-tools to resolve fastq-dump --> ERROR. However, I am still getting error for fastq-dump -X 1 -Z SRR1553591 --> ERROR. Thank you.

ialbert commented 5 months ago

fastq dump is installed separately, made sure to restart the terminal

and to activate the correct environment

babasaraki commented 5 months ago

Thank you Sir for this information. Will rework on it again and see how it goes.