why fastq-dump doesn`t work?

Question

[star]

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

[GenoMax]

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.

[star]

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

[ATpoint]

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

[star]

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

[ATpoint]

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

[star]

Link

[ATpoint]

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

[star]

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

[GenoMax]

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

[star]

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`

[GenoMax]

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.

Please do the same for your previous posts as well.

Answer 1

[ATpoint]

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.