IndexError

[Kiliankleemann]

I installed an ARM64 conda environment and loaded: conda install parallel-fastq-dump 'sra-tools>=3.0.0'

I used this execution: cat SRR_Acc_List.txt | while read sample; do parallel-fastq-dump --sra-id ${sample} --threads 4 --outdir fastq_files/ --split-files --gzip done

Traceback (most recent call last): File "/Users/kiliankleemann/anaconda3/envs/SRA_toolkit/bin/parallel-fastq-dump", line 116, in get_spot_count total += int(l.split('|')[2].split(':')[0])

IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/kiliankleemann/anaconda3/envs/SRA_toolkit/bin/parallel-fastq-dump", line 181, in <module>
    main()
  File "/Users/kiliankleemann/anaconda3/envs/SRA_toolkit/bin/parallel-fastq-dump", line 175, in main
    pfd(args, si, extra_args)
  File "/Users/kiliankleemann/anaconda3/envs/SRA_toolkit/bin/parallel-fastq-dump", line 49, in pfd
    n_spots = get_spot_count(srr_id)
              ^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/kiliankleemann/anaconda3/envs/SRA_toolkit/bin/parallel-fastq-dump", line 122, in get_spot_count
    raise IndexError(msg.format('\n'.join(txt), '\n'.join(etxt)))
IndexError: sra-stat output parsing error!

[rvalieris]

Hello, can you tell me which SRR are you trying to download that produced this error ?

also run this command and show me the output: sra-stat --meta --quick <SRR>

[Lsz-20]

The same question. 2023-09-28T01:08:30 sra-stat.3.0.8 sys: encryption failed while validating token within cryptographic module - Verification issue 0xC for this certificate: ( cert. version : 3 serial number : 0A:75:A4:D0:FD:F0:ED:BF:93:72:16:E5:84:AD:26:CE:F6:6C:B5:75 issuer name : CN=demotest.doctorcom.com, O=Doctorcom LTD., C=CN subject name : CN=demotest.doctorcom.com, O=Doctorcom LTD., C=CN issued on : 2019-09-09 09:20:26 expires on : 2039-10-24 09:20:26 signed using : RSA with SHA-256 RSA key size : 2048 bits basic constraints : CA=true ) 2023-09-28T01:08:30 sra-stat.3.0.8 sys: mbedtls_ssl_get_verify_result for 'locate.ncbi.nlm.nih.gov' returned 0xC ( !! The certificate Common Name (CN) does not match with the expected CN !! The certificate is not correctly signed by the trusted CA ) 2023-09-28T01:08:30 sra-stat.3.0.8 sys: encryption failed while validating token within cryptographic module - Verification issue 0xC for this certificate: ( cert. version : 3 serial number : 0A:75:A4:D0:FD:F0:ED:BF:93:72:16:E5:84:AD:26:CE:F6:6C:B5:75 issuer name : CN=demotest.doctorcom.com, O=Doctorcom LTD., C=CN subject name : CN=demotest.doctorcom.com, O=Doctorcom LTD., C=CN issued on : 2019-09-09 09:20:26 expires on : 2039-10-24 09:20:26 signed using : RSA with SHA-256 RSA key size : 2048 bits basic constraints : CA=true ) 2023-09-28T01:08:30 sra-stat.3.0.8 sys: mbedtls_ssl_get_verify_result for 'locate.ncbi.nlm.nih.gov' returned 0xC ( !! The certificate Common Name (CN) does not match with the expected CN !! The certificate is not correctly signed by the trusted CA ) 2023-09-28T01:08:30 sra-stat.3.0.8 int: directory not found while opening manager within virtual file system module - 'SRR9883230' Perhaps the SRR doc not exist？

[rvalieris]

@Lsz-20 , thats a different error.

the SRR exists and I can't reproduce your issue, this error message suggests a network / firewall issue I think.

[Kiliankleemann]

managed to fix it with the loop calling.

[Lsz-20]

managed to fix it with the loop calling. Maybe we can say more about how to operate it?