Question: why fastq-dump doesn`t work?
0
gravatar for star
20 months ago by
star260
Netherlands
star260 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 • 2.4k views
ADD COMMENTlink modified 20 months ago by ATpoint40k • written 20 months ago by star260
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 20 months ago • written 20 months ago by genomax91k

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

ADD REPLYlink written 20 months ago by star260

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

ADD REPLYlink written 20 months ago by ATpoint40k

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

ADD REPLYlink written 20 months ago by star260
1

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

ADD REPLYlink written 20 months ago by ATpoint40k

Link

ADD REPLYlink modified 20 months ago by ATpoint40k • written 20 months ago by star260
1

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

ADD REPLYlink written 20 months ago by ATpoint40k

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

ADD REPLYlink modified 20 months ago • written 20 months ago by star260

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 20 months ago • written 20 months ago by genomax91k

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 20 months ago • written 20 months ago by star260
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 20 months ago by genomax91k
3
gravatar for ATpoint
20 months ago by
ATpoint40k
Germany
ATpoint40k 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 20 months ago • written 20 months ago by ATpoint40k
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