Entering edit mode
4 weeks ago
popozan
•
0
Hi guys, I am very new to bioinformatics and using the biostar handbook to teach me, Started installing packages, and I came across the error
Unable to run: fastq-dump, bio, fastq-dump -X 1 -Z SRR1553591
On bash, this is the result when I ran doctor.py
:
# Checking symptoms ...
# bwa ... OK
# datamash ... OK
# fastqc -h ... OK
# hisat2 ... OK
# featureCounts ... OK
# efetch ... OK
# esearch ... OK
# samtools ... OK
# fastq-dump --> ERROR
# bowtie2 ... OK
# bcftools ... OK
# seqtk ... OK
# seqkit ... OK
# bio --> ERROR
# fastq-dump -X 1 -Z SRR1553591 --> ERROR
#
# Found some problems
#
# Unable to run: fastq-dump, bio, fastq-dump -X 1 -Z SRR1553591
#
# Check the Biostar Handbook for installation help.
#
#
# Warning: the ~/bin folder is not in your PATH!
Any advice?
I have never run this, can you try fastq- dump error message
Please create an issue with this error at Biostars handbook issues page: https://github.com/biostars/biostar-handbook/issues