Can fastq-dump be run without an internet connection?

Question

[will.townes]

Let's say I have an SRA file previously downloaded to a local filesystem by using prefetch from SRA toolkit, but I don't have internet access. Theoretically, I should be able to convert it into FASTQ format using either fastq-dump or fasterq-dump. However, both of these throw errors like

error from srapath:
Error: RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound)

I have confirmed that the conversion works fine when internet is enabled (using SRR000001 as a test). Why does fastq-dump need to access the internet here? And is there a way to get it to work without the internet access, perhaps by telling it not to check the srapath?

Answer 1

[wm]

You can try the version fastq-dump v2.9.6-1 without internet. https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit

The latest version of fastq-dump v2.10.4 requires internet access. if not, it will throw the follow error message.

# disconnect the internet

# v2.9.6, works
$ fastq-dump --split-3 SRR10259334.sra
Read 3232411 spots for SRR10259334.sra
Written 3232411 spots for SRR10259334.sra

# v2.10.4, failed
$ fastq-dump --split-3 SRR10259334.sra
failed to call external services.

Anyway, the error message is not the same as yours.

I did not repeat your error. You could have a try, using the same version prefetch and fastq-dump.

[Ram]

You can try the version fastq-dump v2.9.6-1 without internet.

Did you try it? Does it work?

[wm]

Yes, I tried it on my PC and it works.

# network disconnected
$ ping 114.114.114.114
connect: Network is unreachable

$ fastq-dump --version

fastq-dump : 2.9.6

$ fasterq-dump --version

fasterq-dump : 2.9.6


# run fastq-dump
$ fastq-dump --split-3 SRR10259334.sra
Read 3232411 spots for SRR10259334.sra
Written 3232411 spots for SRR10259334.sra

$ ls -lh
-rw-r--r-- 1 ming ming  983145852 3月  18 10:23 SRR10259334_1.fastq
-rw-r--r-- 1 ming ming  983145852 3月  18 10:23 SRR10259334_2.fastq
-rw-r--r-- 1 ming ming  259666170 3月  18 10:21 SRR10259334.sra


# run fasterq-dump
$ fasterq-dump -p -3 SRR10259334.sra
join   :|-------------------------------------------------- 100.00%
concat :|-------------------------------------------------- 100.00%
spots read      : 3,232,411
reads read      : 6,464,822
reads written   : 6,464,822

$ ls -lh
-rw-r--r-- 1 ming ming  983145852 3月  18 10:23 SRR10259334_1.fastq
-rw-r--r-- 1 ming ming  983145852 3月  18 10:23 SRR10259334_2.fastq
-rw-r--r-- 1 ming ming  259666170 3月  18 10:21 SRR10259334.sra
-rw-r--r-- 1 ming ming 1009005140 3月  18 10:24 SRR10259334.sra_1.fastq
-rw-r--r-- 1 ming ming 1009005140 3月  18 10:24 SRR10259334.sra_2.fastq

[wm]

Anyway, I do not understand, why fastq-dump and fasterq-dump require internet access in the latest version: 2.10.4.

[will.townes]

Thanks so much, this is very useful to know! If others have a similar difficulty, please chime in here to encourage NCBI to allow the newer version of SRA-tools to work without internet connection when dealing with already downloaded files. https://github.com/ncbi/sra-tools/issues/302