nana-marinbio commented 9 months ago

When ran doctor.py I got fastq-dump error, below.

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.

I tried $ make vcf CPU=2 and got the following error:

fastq-dump -F -X 10000 --split-files -O reads SRR1553425 dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin Referenced from: /Users/anapaulabmoreira/bin/sratoolkit.3.0.0-mac64/bin/fastq-dump (which was built for Mac OS X 10.15) Expected in: /usr/lib/libSystem.B.dylib

ialbert commented 9 months ago

what is your MacOS version?

also can you check whether the latest sratools works?

https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit