Question: why fastq-dump doesn`t work?
0
gravatar for star
7 weeks ago by
star130
Netherlands
star130 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 • 308 views
ADD COMMENTlink modified 7 weeks ago by ATpoint14k • written 7 weeks ago by star130
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 7 weeks ago • written 7 weeks ago by genomax64k

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

ADD REPLYlink written 7 weeks ago by star130

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

ADD REPLYlink written 7 weeks ago by ATpoint14k

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

ADD REPLYlink written 7 weeks ago by star130
1

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

ADD REPLYlink written 7 weeks ago by ATpoint14k

Link

ADD REPLYlink modified 7 weeks ago by ATpoint14k • written 7 weeks ago by star130
1

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

ADD REPLYlink written 7 weeks ago by ATpoint14k

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

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by star130

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 7 weeks ago • written 7 weeks ago by genomax64k

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 7 weeks ago • written 7 weeks ago by star130
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 7 weeks ago by genomax64k
3
gravatar for ATpoint
7 weeks ago by
ATpoint14k
Germany
ATpoint14k 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 7 weeks ago • written 7 weeks ago by ATpoint14k
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