[Sciapps-support] Cannot chk error status number - Tool: SRATool

[Wang, Liya]

Hi Cynthia,

Sorry that I just checked and found that NCBI stopped supporting ftp based downloading a few months ago, which made the app failed. I have removed the app from SciApps.

But you can use a CyVerse app to download the data to your CyVerse data store and the tutorial is here: https://learning.cyverse.org/projects/cyverse-importing-sradata-quickstart/en/latest/

Regards,
Liya

On May 4, 2020, at 2:26 PM, Cynthia SC <cyntsc10 at gmail.com<mailto:cyntsc10 at gmail.com>> wrote:

Hi, me again

Now, I can execute the query SRA_Tool, but another error comes up...

No such directory ‘sra/sra-instant/reads/ByRun/sra/SRR/SRR218/SRR2185181’.

2020-05-04T18:08:14 fastq-dump.2.8.2 err: item not found while constructing within virtual database module - the path 'SRR2185181.sra' cannot be opened as database or table
mv: cannot stat ‘SRR2185181.fastq.gz’: No such file or directory

I am sure the SRR# exists, Do I need create another directory? or, what is happening?... How do I solve this issue?

Thanks,
Cynthia SC

<Captura de pantalla de 2020-05-04 13-24-42.png>




El lun., 4 may. 2020 a las 12:55, Cynthia SC (<cyntsc10 at gmail.com<mailto:cyntsc10 at gmail.com>>) escribió:
Ready, Thanks a lot!

Cynthia SC

El lun., 4 may. 2020 a las 12:38, Wang, Liya (<wangli at cshl.edu<mailto:wangli at cshl.edu>>) escribió:
Hi Cynthia,

You need to have the sci_data folder in your CyVerse home folder (/iplant/home/cyntsc/sci_data), or follow the instruction below to let CyVerse create the folder for you.
https://learning.cyverse.org/projects/sciapps_guide/en/latest/step2.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__learning.cyverse.org_projects_sciapps-5Fguide_en_latest_step2.html&d=DwMFaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=VpyaB_1D0rsMuMrIznuCSA&m=5SySHOqpHr5epnq5a_-lVlipgLf0usixzL59lu72pRA&s=ao1z_DimEG6PVHzVfDxsEEOwCY5qE6hC_ULRDVa7fEk&e=>

Liya

On May 4, 2020, at 12:24 PM, Cynthia SC <cyntsc10 at gmail.com<mailto:cyntsc10 at gmail.com><mailto:cyntsc10 at gmail.com<mailto:cyntsc10 at gmail.com>>> wrote:

Hi!

I am trying to download this fasta file : SRR7686004, using the Query submenu SRA_Tool
Previous to submit the job, I created a sci_data folder as required for the tool, but any way a job status error es got it
I check in the right panel and in the workflow/Myjobs for a clue about the error, but there is not additional information about it.

I attached you some images for your reference...

Thanks by advance

Cynthia SC
<Captura de pantalla de 2020-05-04 11-14-35.png>


--
MCC. Cynthia Soto Cardinault
Estudiante de Doctorado
Unidad de Biotecnología
CICY
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--
MCC. Cynthia Soto Cardinault
Estudiante de Doctorado
Unidad de Biotecnología
CICY


--
MCC. Cynthia Soto Cardinault
Estudiante de Doctorado
Unidad de Biotecnología
CICY