Question: why fastq-dump doesn`t work?
0
gravatar for star
12 months ago by
star200
Netherlands
star200 wrote:

I am trying to convert .sra format to .fastq one but I faced with below error. I could do it before but it doesn`t work now!

It woks on other data like "SRR8502555.sra'' but for other ones does not work (I got these SRAs from dbGAP after filing related forms and getting permission).

  :~$ /home/Softwar/sratoolkit.2.9.2-centos_linux64/bin/fastq-dump --gzip --split-files /home/Projects/Project_enhancer/ATAC_seq/Torre-Ubieta_2018_ATAC.seq/ATAC_seq_paired/data/SRR6208926.sra 

2019-01-31T12:36:30 fastq-dump.2.9.2 err: item not found while constructing within virtual database module - the path '/home/Projects/Project_enhancer/ATAC_seq/Torre-Ubieta_2018_ATAC.seq/ATAC_seq_paired/data/SRR6208926.sra' cannot be opened as database or table
fastq-dump prefetch sra • 1.2k views
ADD COMMENTlink modified 12 months ago by ATpoint28k • written 12 months ago by star200
2

Because Projects/Project_enhancer/ATAC_seq/Torre-Ubieta_2018_ATAC.seq/ATAC_seq_paired/data/SRR6208926.sra is not a valid path. Are you missing a leading / or is that directory under one where you are running this command from.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax77k

Thanks for your reply. I run it one more time from first directory but I got with the same error.

ADD REPLYlink written 12 months ago by star200

For restricted data, you have to execute the command from within the directory that you specified in vdb-config.

ADD REPLYlink written 12 months ago by ATpoint28k

you mean I should perform fastq-dump from usr/bin/

ADD REPLYlink written 12 months ago by star200
1

No, please make a screenshort from vdb-config -i and share it here.

ADD REPLYlink written 12 months ago by ATpoint28k

Link

ADD REPLYlink modified 12 months ago by ATpoint28k • written 12 months ago by star200
1

Right, so go into the dbGaP folder, copy the SRAs to this one and start fastq-dump from there.

ADD REPLYlink written 12 months ago by ATpoint28k

Great! It is working!! Thank you very much :).

ADD REPLYlink modified 12 months ago • written 12 months ago by star200

It would be the default import directory you chose when running vdb-config. Did you use /usr/bin? That would be an odd choice.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax77k

Yes I have done it and get this error:

:/usr/bin$ fastq-dump /home/Projects/Project_enhancer/ATAC_seq/Torre-Ubieta_2018_ATAC.seq/ATAC_seq_paired/data/SRR6208926.sra

`2019-01-31T14:11:00 fastq-dump.2.8.2 err: libs/kfs/sra.c:110:SraHeaderValidate: item not found while constructing within virtual database module - the path '/home/Projects/Project_enhancer/ATAC_seq/Torre-Ubieta_2018_ATAC.seq/ATAC_seq_paired/data/SRR6208926.sra' cannot be opened as database or table`
ADD REPLYlink modified 12 months ago • written 12 months ago by star200
1

star :

Don't forget to follow up on your threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

Please do the same for your previous posts as well.

ADD REPLYlink written 12 months ago by genomax77k
3
gravatar for ATpoint
12 months ago by
ATpoint28k
Germany
ATpoint28k wrote:

Bottom line of the above comments: When downloading restricted data from dbGaP, you must be inside the specified dbGaP folder (check vdb-config -i) otherwise fastq-dump will reject file conversion.

ADD COMMENTlink modified 12 months ago • written 12 months ago by ATpoint28k
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