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SRR6305512 - Cannot KStblHttpFileRead error #689

Closed xexpanderx closed 1 year ago

xexpanderx commented 2 years ago

Hello!

I have an issue trying to extract the fastq-file from this sample: SRR6305512. It works with all other samples within the same project, except this one. I am using version 2.11.0, but I also tried with latest 3.x.

Any idea why? Thank you!

prefetch --ngc prj_17325.ngc SRR6305512

2022-08-03T09:05:27 prefetch.2.11.0: 1) Downloading 'SRR6305512'...
2022-08-03T09:05:27 prefetch.2.11.0:  Downloading via HTTPS...
2022-08-03T09:05:40 prefetch.2.11.0 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
klymenko commented 2 years ago

Download the latest toolkit.

xexpanderx commented 2 years ago

Unfortunately, as I already mentioned, I did try with 3.0.0 as well, same error.

klymenko commented 2 years ago

Please email to sra@ncbi.nlm.nih.gov.

hyjforesight commented 2 years ago

same issue, any ideas? Thanks!

klymenko commented 1 year ago

@xexpanderx, @hyjforesight, do you still need help?

b-lac commented 1 year ago

Same issue for me:

 prefetch -O ./ -X 1T --ngc key.ngc SRR3088428

  2022-12-02T10:17:48 prefetch.3.0.1: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
  2022-12-02T10:17:48 prefetch.3.0.1: 1) Downloading 'SRR3088428'...
  2022-12-02T10:17:53 prefetch.3.0.1: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
  2022-12-02T10:17:53 prefetch.3.0.1:  Downloading via HTTPS...
  2022-12-02T10:18:49 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:19:26 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:20:12 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:20:55 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:21:34 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:22:30 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:23:13 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:24:08 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:25:40 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:26:38 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T10:27:51 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead                                                                         
  2022-12-02T10:31:58 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead                                                                         
  2022-12-02T10:33:38 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead                                                                         
  2022-12-02T10:36:20 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead                                                                         
  2022-12-02T10:48:58 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead                                                                         
  2022-12-02T10:57:36 prefetch.3.0.1 err: data unexpected while reading file within network system module - Cannot KStblHttpFileRead
  2022-12-02T11:37:40 prefetch.3.0.1 err: file no permission while reading file within file system module - Cannot KFileRead 'https://trace.ncbi.nlm.nih.gov/Traces/sdlr/sdlr.fcgi?jwt=eyJhbGciOiJSUzI1NiIsImtpZCI6InNkbHJraWQxIiwidHlwIjoiSldUIn0.eyJhY2MiOiJTUlIzMDg4NDI4IiwiZXhwIjoxNjY5OTkwNjYzLCJmaWxlU2l6ZSI6IjUwMDM1MTM3OTMiLCJpYXQiOjE2Njk5NzYyNjMsImlnbm9yZUNlIjoidHJ1ZSIsImp0aSI6IjYwN2I3NGIxLTI4ZGUtNGZkNi1iYWIzLWM1YTZlM2FjZjk5NiIsImxpbmsiOiJodHRwczovL3NyYS1jYS1ydW4tb2RwLnMzLmFtYXpvbmF3cy5jb20vc3JhL3BoczAwMTAyNy5jMS9TUlIzMDg4NDI4L1NSUjMwODg0Mjg_eC1hbXotcmVxdWVzdC1wYXllcj1yZXF1ZXN0ZXImbmNiaV9waGlkPUEzQzM5QkVBOTBCMzQzMTUwMDAwMjYwNTdBNjc1RkM2LjEuMSZwcm9qZWN0X2lkPTMxNDU2IiwicmVnaW9uIjoidXMtZWFzdC0xIiwic2VydmljZSI6InMzIiwic2lnbmluZ0FjY291bnQiOiJzcmFfczNfY2Ffb2RwIiwidGltZW91dCI6MTQ0MDB9.JNEADVCrgJirIJm66jqNzcLu63usNg3fg6zbQeeyvvE-b0eZqxkGYbAkHkhyu-xHnkQMe8wzava_n7t8cfP1Tl2XxTZR-EFexBsg8uC0wXBLCEKnD3MPq-zyzwP7t9nMe_kw3C7_Ru475udya20XRBhqA9NUg38P1QSg8A8zGgg79Z45h90dO72q0BAXJ3Fi_V7PhihNChlT0s7o4EjIJSCP9NBrosni3ZuwgafIAavtj8YB82Jt_DjjM1COBCdrKBjzVoRIirwBzdT82g6DQrFwjpe2d1D6j6new9VwAIXiZ8loVilvpjDmboVd2cVUC3IVWCUxMxR3OxKJgCdihg': sz=3768, to=1920
  2022-12-02T11:37:48 prefetch.3.0.1:  HTTPS download failed
  2022-12-02T11:38:02 prefetch.3.0.1: 1) failed to download 'SRR3088428': RC(rcFS,rcFile,rcReading,rcFile,rcNoPerm)

I'm using the latest version (3.0.1) of sra-tools, also the command works well for the other SRA I need to download.

klymenko commented 1 year ago

Please send an email to sra@ncbi.nlm.nih.gov .

klymenko commented 1 year ago

@xexpanderx , do you need more help?