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Fastq-dump err: directory not found while opening manager within virtual file system module #964

Closed hhtiantt closed 1 month ago

hhtiantt commented 2 months ago

I am currently running sratoolkit 3.1.1 and have run into the following error:

~/anaconda3/envs/new_env/bin/fastq-dump ./PRJNA870935/raw_data/SRR21148806 -O ./PRJNA870935 --split-3

2024-08-31T15:06:25 fastq-dump.3.1.1 warn: directory not found while opening manager within virtual file system module - can't open NC_000001.11 as a RefSeq or as a WGS
2024-08-31T15:06:25 fastq-dump.3.1.1 err: directory not found while opening manager within virtual file system module - failed ./PRJNA870935/raw_data/SRR21148806

I have been stuck on this problem for several days now and have not been able to find any resources that could help me resolve it. Thus, any assistance you could provide would be greatly appreciated.

Thank you.

klymenko commented 2 months ago

Run ~/anaconda3/envs/new_env/bin/prefetch ./PRJNA870935/raw_data/SRR21148806 first.

hhtiantt commented 2 months ago

Run ~/anaconda3/envs/new_env/bin/prefetch ./PRJNA870935/raw_data/SRR21148806 first.

Thank you for your answer. I tried prefetch, but it still reported an error.

2024-09-03T12:39:57 prefetch.3.1.1: 1) Resolving './PRJNA870935/raw_data/SRR21148806'...
'./PRJNA870935/raw_data/SRR21148806' is a local non-kart file
2024-09-03T12:39:59 prefetch.3.1.1: './PRJNA870935/raw_data/SRR21148806' has 127 unresolved dependencies
2024-09-03T12:39:59 prefetch.3.1.1 int: connection not found while validating within network system module - cannot get remote location for 'NC_000001.11'
klymenko commented 2 months ago

Do you have internet access?