prefetch - failed to verify error

[uasic]

Hello,
I am trying to download only some runs from PRJNA688881 with the following command:

.\prefetch --output-directory healthy_sra -p -H 5 SRR13336836 SRR13336835 SRR13336834 SRR13336833 SRR13336832 SRR13336830 SRR13336829 SRR13336831 SRR13336826 SRR13336882 SRR13336825 SRR13336887 SRR13336885 SRR13336883 SRR13336881 SRR13336871 SRR13336880 SRR13336879 SRR13336877 SRR13336876 SRR13336933 SRR13336875 SRR13336866 SRR13336873 SRR13336870 SRR13336860 SRR13336859 SRR13336868 SRR13336862 SRR13336867 SRR13336902 SRR13336900 SRR13336858 SRR13336898 SRR13336901 SRR13336896 SRR13336894 SRR13336856 SRR13336892 SRR13336853 SRR13336891 SRR13336893 SRR13336889 SRR13336886 SRR13336888 SRR13336852

In case of most of the downloaded samples I have received following error:
2024-03-23T10:46:11 prefetch.3.0.7 int: no error - failed to verify
2024-03-23T10:46:11 prefetch.3.0.7: 1) failed to download 'SRR13336836': RC(rcFS,rcFile,rcReading,rcFile,rcCorrupt)

Similar problem was described here: #568.

.sra files are downloaded together with .sra.prf files in each folder.

If I run curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR13336836 I get this output:

StatusCode : 200
StatusDescription : OK
Content : {"version": "2","result": [{"bundle": "SRR13336836","status": 200,"msg": "ok","files": [{"object":
"srapub|SRR13336836","accession": "SRR13336836","type": "sra","name": "SRR13336836","size":
505702978...
RawContent : HTTP/1.1 200 OK
Strict-Transport-Security: max-age=31536000; includeSubDomains; preload
Referrer-Policy: origin-when-cross-origin
Content-Security-Policy: upgrade-insecure-requests
NCBI-SID: 890F3...
Forms : {}
Headers : {[Strict-Transport-Security, max-age=31536000; includeSubDomains; preload], [Referrer-Policy,
origin-when-cross-origin], [Content-Security-Policy, upgrade-insecure-requests], [NCBI-SID,
890F3B9A5FEFC2E1_0015SID]...}
Images : {}
InputFields : {}
Links : {}
ParsedHtml : mshtml.HTMLDocumentClass
RawContentLength : 426

Thank you in advance.

[klymenko]

What is the full output of curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR13336836 ?
You truncated Content JSON.

Are you running on Windows? What terminal program do you use?

[uasic]

The truncated output above was the output of curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR13336836 in PowerShell.

This is output from git bash:

{
"version": "2",
"result": [
{
"bundle": "SRR13336836",
"status": 200,
"msg": "ok",
"files": [
{
"object": "srapub|SRR13336836",
"accession": "SRR13336836",
"type": "sra",
"name": "SRR13336836",
"size": 5057029785,
"md5": "bffa179a068bf7203d19a93bdeab9e63",
"modificationDate": "2021-01-01T15:18:04Z",
"locations": [
{
"service": "s3",
"region": "us-east-1",
"link": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13336836/SRR13336836"
}
]
}
]
}
]
}

For downloading I was always using PowerShell.

[klymenko]

what is the output of:
srapath SRR13336836

[uasic]

GitBash:
bash: srapath: command not found

PowerShell:
srapath : The term 'srapath' is not recognized as the name of a cmdlet, function, script file, or operable program.
Check the spelling of the name, or if a path was included, verify that the path is correct and try again.
At line:1 char:1

• srapath SRR13336836

•   + CategoryInfo          : ObjectNotFound: (srapath:String) [], CommandNotFoundException
    + FullyQualifiedErrorId : CommandNotFoundException
  

[klymenko]

run it from the same directory where you ran prefetch

[uasic]

https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13336836/SRR13336836 (PowerShell, still not found in Bash)

[klymenko]

Was SRR13336836 directory created in directory where you ran prefetch?

[uasic]

Yes - download creates SRR13336836 folder with .sra file and .sra.prf.

More detailes below:

This is the command I run, with error:

Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.

Install the latest PowerShell for new features and improvements! https://aka.ms/PSWindows

PS E:\phd-sekvence\wgs> prefetch --output-directory healthy_sra -p -H 5 SRR13336836 SRR13336835 SRR13336834 SRR13336833 SRR13336832 SRR13336830 SRR13336829 SRR13336831 SRR13336826 SRR13336882 SRR13336825 SRR13336887 SRR13336885 SRR13336883 SRR13336881 SRR13336871 SRR13336880 SRR13336879 SRR13336877 SRR13336876 SRR13336933 SRR13336875 SRR13336866 SRR13336873 SRR13336870 SRR13336860 SRR13336859 SRR13336868 SRR13336862 SRR13336867 SRR13336902 SRR13336900 SRR13336858 SRR13336898 SRR13336901 SRR13336896 SRR13336894 SRR13336856 SRR13336892 SRR13336853 SRR13336891 SRR13336893 SRR13336889 SRR13336886 SRR13336888 SRR1333685

2024-03-26T08:30:27 prefetch.3.0.7: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-03-26T08:30:27 prefetch.3.0.7: 1) Downloading 'SRR13336836'...
2024-03-26T08:30:28 prefetch.3.0.7: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-26T08:30:28 prefetch.3.0.7: Downloading via HTTPS...
|-------------------------------------------------- 100%
2024-03-26T10:09:22 prefetch.3.0.7: HTTPS download succeed
2024-03-26T10:09:22 prefetch.3.0.7: verifying 'SRR13336836'...
2024-03-26T10:40:21 prefetch.3.0.7 int: no error - failed to verify
2024-03-26T10:40:21 prefetch.3.0.7: 1) failed to download 'SRR13336836': RC(rcFS,rcFile,rcReading,rcFile,rcCorrupt)

ls and pwd commands:

PS E:\phd-sekvence\wgs> pwd

Path

E:\phd-sekvence\wgs

PS E:\phd-sekvence\wgs> ls

Directory: E:\phd-sekvence\wgs

Mode LastWriteTime Length Name

---

d----- 18. 02. 2024 13:46 PRJNA516054_fastq
d----- 27. 02. 2024 20:22 PRJNA686821_fastq
d----- 27. 02. 2024 20:22 PRJNA686821_sra
d----- 27. 02. 2024 20:22 PRJNA782533_fastq
d----- 27. 02. 2024 20:23 PRJNA782533_sra
d----- 27. 02. 2024 20:23 PRJNA895372_fastq
d----- 27. 02. 2024 20:23 PRJNA895372_sra
d----- 27. 02. 2024 20:23 PRJNA530620_fastq
d----- 27. 02. 2024 20:23 PRJNA530620_sra
d----- 27. 02. 2024 20:23 PRJNA845014_fastq
d----- 27. 02. 2024 20:24 PRJNA845014_sra
d----- 27. 02. 2024 21:12 healthy_sra
d----- 27. 02. 2024 21:13 healthy_fastq
d----- 1. 03. 2024 08:00 ponavljanje_fastq
d----- 24. 03. 2024 17:50 sra_533_done
d----- 26. 03. 2024 10:26 fasterq.tmp..0
-a---- 26. 03. 2024 10:26 1276 sra2fastq.py
-a---- 15. 03. 2024 19:15 1271 sra2fastq2.py

PS E:\phd-sekvence\wgs>

[klymenko]

What is the size and md5 of SRR13336836/SRR13336836.sra?

[uasic]

The size iz 4,9 GB and md5 from PowerShell is:

PS E:\phd-sekvence\wgs\healthy_sra\SRR13336836> ls


    Directory: E:\phd-sekvence\wgs\healthy_sra\SRR13336836


Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
-a----      26. 03. 2024     11:09            160 SRR13336836.sra.prf
-a----      26. 03. 2024     11:09     5057029785 SRR13336836.sra


PS E:\phd-sekvence\wgs\healthy_sra\SRR13336836> Get-FileHash .\SRR13336836.sra -Algorithm MD5

Algorithm       Hash                                                                   Path
---------       ----                                                                   ----
MD5             1EE3F0353FBCD5B95B88E4E535206A0F                                       E:\phd-sekvence\wgs\healthy_s...


PS E:\phd-sekvence\wgs\healthy_sra\SRR13336836> Get-FileHash .\SRR13336836.sra.prf -Algorithm MD5

Algorithm       Hash                                                                   Path
---------       ----                                                                   ----
MD5             5B81AEFC2FD38329285E352DBBFF3489                                       E:\phd-sekvence\wgs\healthy_s...

[klymenko]

md5 of downloaded SRR13336836 does not match provided by SDL.

[klymenko]

What is the output of the following:
certutil -hashfile SRR13336836.sra MD5

[klymenko]

Do you run it on cloud?

[klymenko]

Where did you get sratoolkit?

[uasic]

PS F:\sratoolkit.3.1.0-win64\bin> certutil -hashfile SRR13336836.sra MD5
CertUtil: -hashfile command FAILED: 0x80070002 (WIN32: 2 ERROR_FILE_NOT_FOUND)
CertUtil: The system cannot find the file specified.

or

PS F:\sratoolkit.3.0.7-win64\bin> certutil -hashfile SRR13336836.sra MD5
CertUtil: -hashfile command FAILED: 0x80070002 (WIN32: 2 ERROR_FILE_NOT_FOUND)
CertUtil: The system cannot find the file specified.
PS F:\sratoolkit.3.0.7-win64\bin>

I do not run it on cloud - locally on my computer, saving them directly on external hard drive.

sratoolkit was downloaded from GitHub:
https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit

I've also tried download sequences from PRJNA845014 during the night, same error in the morning:

PS F:\sratoolkit.3.1.0-win64\bin> .\prefetch --output-directory F:\phd-sekvence\wgs\PRJNA845014_sra -p -H 5 PRJNA845014
2024-03-26T20:10:32 prefetch.3.1.0 int: string unexpected while executing query within virtual file system module - multiple response SRR URLs for the same service 's3'
2024-03-26T20:12:23 prefetch.3.1.0: 1) Downloading 'SRR19537292'...
2024-03-26T20:12:43 prefetch.3.1.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-26T20:12:44 prefetch.3.1.0:  Downloading via HTTPS...
|-------------------------------------------------- 100%
2024-03-26T20:32:20 prefetch.3.1.0:  HTTPS download succeed
2024-03-26T20:32:21 prefetch.3.1.0:   verifying 'SRR19537292'...
2024-03-26T20:42:14 prefetch.3.1.0:  'SRR19537292' is valid
2024-03-26T20:42:14 prefetch.3.1.0: 1) 'SRR19537292' was downloaded successfully
2024-03-26T20:42:14 prefetch.3.1.0: 1) Downloading 'SRR19537293'...
2024-03-26T20:42:15 prefetch.3.1.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-03-26T20:42:15 prefetch.3.1.0:  Downloading via HTTPS...
|-------------------------------------------------- 100%
2024-03-26T21:11:38 prefetch.3.1.0:  HTTPS download succeed
2024-03-26T21:11:38 prefetch.3.1.0:   verifying 'SRR19537293'...
2024-03-26T21:30:01 prefetch.3.1.0 int: no error - failed to verify
2024-03-26T21:30:01 prefetch.3.1.0: 1) failed to download 'SRR19537293': RC(rcFS,rcFile,rcReading,rcFile,rcCorrupt)

PS F:\sratoolkit.3.1.0-win64\bin> certutil -hashfile SRR13336836.sra MD5
CertUtil: -hashfile command FAILED: 0x80070002 (WIN32: 2 ERROR_FILE_NOT_FOUND)
CertUtil: The system cannot find the file specified.
PS F:\sratoolkit.3.1.0-win64\bin>