prefetch - failed to verify error #920
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What is the full output of Are you running on Windows? What terminal program do you use? |
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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: { For downloading I was always using PowerShell. |
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what is the output of: |
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GitBash: PowerShell:
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run it from the same directory where you ran |
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https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13336836/SRR13336836 (PowerShell, still not found in Bash) |
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Was |
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Yes - download creates SRR13336836 folder with .sra file and .sra.prf. More detailes below: This is the command I run, with error: Windows PowerShell 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. ls and pwd commands: PS E:\phd-sekvence\wgs> pwd PathE:\phd-sekvence\wgs PS E:\phd-sekvence\wgs> ls Mode LastWriteTime Length Name d----- 18. 02. 2024 13:46 PRJNA516054_fastq PS E:\phd-sekvence\wgs> |
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What is the size and md5 of |
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The size iz 4,9 GB and md5 from PowerShell is: |
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md5 of downloaded SRR13336836 does not match provided by SDL. |
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What is the output of the following: |
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Do you run it on cloud? |
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Where did you get sratoolkit? |
or I do not run it on cloud - locally on my computer, saving them directly on external hard drive. sratoolkit was downloaded from GitHub: I've also tried download sequences from PRJNA845014 during the night, same error in the morning: |
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What version of Windows do you have? Did you succeed to download any run? |
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@uasic, do you need help? |
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Sorry for late reply - I am out of office till Sunday. I need to check about the windows but I think it is windows 11. From sequences above, SRR19537292 was downloaded without any errors. The same command gave error for the next sequence (SRR19537293). |
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What is the output of the following? |
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One correction - I have Windows 10 Home on this computer. The output is: |
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@uasic, please run the following and post the full output: |
I have also tried to download sra file directly on external drive and have not received any error. At the moment, the transfer seems to be working so I will try downloading the other sequences as well and will report the outcome. For now - thank you very much for all your help and patience :) |
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Run |
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I've managed to download quite few sequences without any errors, till yesterday when first few .sra files from PRJNA845014 were downloaded successfully, but after that I get the same error (output 1) . Using -fy saves files directly on my computer and does not work, if I try to save file directly on external drive (outputs 2 and 3). |
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There seems to be an issue on Windows. |
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Thank you! :) |
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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.
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