search

pepkit / geofetch

Builds a PEP from SRA or GEO accessions
https://pep.databio.org/geofetch/
BSD 2-Clause "Simplified" License
45 stars 5 forks source link

Report error in downloading SRA data #112

Closed GuohuaZhu closed 1 year ago

GuohuaZhu commented 1 year ago

Thanks for your newest tools for GEO data downloading！ Today， I had tried it in my shell terminal. It was so nice in download GEO data. However, there was something wrong in downloading SRA data. Could you help me with it? The codes were following:

geofetch -i GSE67303 -n red_algae -m  `pwd`
Metadata folder: /home/users/data/biotreework/geofetch/sra/red_algae
Trying GSE67303 (not a file) as accession...
Skipped 0 accessions. Starting now.
Processing accession 1 of 1: 'GSE67303'
Found previous GSE file: /home/users/data/biotreework/geofetch/sra/red_algae/GSE67303_GSE.soft
Found previous GSM file: /home/users/data/biotreework/geofetch/sra/red_algae/GSE67303_GSM.soft
Processed 4 samples.
Expanding metadata list...
Found SRA Project accession: SRP056574
Found SRA metadata, opening..
Parsing SRA file to download SRR records
Getting SRR: SRR1930183  in (GSE67303)

2023-03-02T09:43:47 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:43:47 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:43:47 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930183' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:43:49 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:43:49 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:43:49 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930183' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:43:54 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:43:54 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:43:54 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930183' cannot be found.
Error occurred while downloading SRA file: Prefetch retries of SRR1930183 failed. Try this sample later
Getting SRR: SRR1930184  in (GSE67303)

2023-03-02T09:43:54 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:43:54 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:43:54 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930184' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:43:57 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:43:57 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:43:57 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930184' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:44:01 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:01 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:01 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930184' cannot be found.
Error occurred while downloading SRA file: Prefetch retries of SRR1930184 failed. Try this sample later
Getting SRR: SRR1930185  in (GSE67303)

mbedtls_ssl_handshake returned -99842023-03-02T09:44:02 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:02 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:02 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930185' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:44:05 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:05 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:05 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930185' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:44:09 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:09 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:09 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930185' cannot be found.
Error occurred while downloading SRA file: Prefetch retries of SRR1930185 failed. Try this sample later
Getting SRR: SRR1930186  in (GSE67303)

2023-03-02T09:44:10 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:10 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:10 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930186' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:44:12 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:12 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:12 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930186' cannot be found.
Prefetch attempt failed, wait a few seconds to try again

2023-03-02T09:44:17 prefetch.2.8.0 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -9984 ( X509 - Certificate verification failed, e.g. CRL, CA or signature check failed )
2023-03-02T09:44:17 prefetch.2.8.0 sys: mbedtls_ssl_get_verify_result returned 0x8 (  !! The certificate is not correctly signed by the trusted CA  )
2023-03-02T09:44:17 prefetch.2.8.0 err: path not found while resolving tree within virtual file system module - 'SRR1930186' cannot be found.
Error occurred while downloading SRA file: Prefetch retries of SRR1930186 failed. Try this sample later
Finished processing 1 accession(s)
Creating complete project annotation sheets and config file...
Sample annotation sheet: /home/users/data/biotreework/geofetch/sra/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!
File has been saved successfully
  Config file: /home/users/data/biotreework/geofetch/sra/red_algae/GSE67303_PEP/GSE67303_PEP.yaml

Thanks a lot！

khoroshevskyi commented 1 year ago

Hi. Thank you for mentioning this error. It seems that this problem is occurring in prefetch (sra toolkit).

I just executed exactly same command and didn't have any errors.

One of the reasons why this error occurs can be old version of sra-toolkit. Can you try to update it. Now you are using prefetch.2.8.0, however prefetch.2.11.3 is avaliabe.

GuohuaZhu commented 1 year ago

Thanks a lot for your timely response. I had updated the prefetch 2.8.0 to 3.0.3, It worked.

……
Sample annotation sheet: 
/home/users/data/biotreework/geofetch/sra/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!
File has been saved successfully
  Config file: /home/users/data/biotreework/geofetch/sra/red_algae/GSE67303_PEP/GSE67303_PEP.yaml
khoroshevskyi commented 1 year ago

Error was fixed.