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rvalieris / parallel-fastq-dump

parallel fastq-dump wrapper
MIT License
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IndexError: sra-stat output parsing error! #55

Open Naturalist1986 opened 10 months ago

Naturalist1986 commented 10 months ago

Hi, I'm installed parallel-fastq-dump on a cluster using SLURM, but i get this error:

(srr_download) moshea@moriah-gw-01:~$ parallel-fastq-dump --sra-id SRR2244401 --threads 4 --outdir . --split-files --gzip -T . 2024-01-07 12:31:15,300 - SRR ids: ['SRR2244401'] 2024-01-07 12:31:15,300 - extra args: ['--split-files', '--gzip'] 2024-01-07 12:31:15,304 - tempdir: /sci/home/moshea/pfd_xr6lq4eh 2024-01-07 12:31:15,304 - CMD: sra-stat --meta --quick SRR2244401 Traceback (most recent call last): File "/sci/home/moshea/miniconda3/envs/srr_download/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 "/sci/home/moshea/miniconda3/envs/srr_download/bin/parallel-fastq-dump", line 181, in <module>
    main()
  File "/sci/home/moshea/miniconda3/envs/srr_download/bin/parallel-fastq-dump", line 175, in main
    pfd(args, si, extra_args)
  File "/sci/home/moshea/miniconda3/envs/srr_download/bin/parallel-fastq-dump", line 49, in pfd
    n_spots = get_spot_count(srr_id)
              ^^^^^^^^^^^^^^^^^^^^^^
  File "/sci/home/moshea/miniconda3/envs/srr_download/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!
--sra-stat STDOUT--

--sra-stat STDERR--

It works on  a private server, but not on the cluster. Can you help?
rvalieris commented 10 months ago

Hello,

this could be a version or network issue, first check that you have the latest version of sra-tools and try this command: sra-stat --meta --quick SRR2244401

you should get this output: SRR2244401|D23G3.1|110485:22317970:22317970|:|:|:

Naturalist1986 commented 10 months ago

This gives a similar error:

(srr_download) moshea@moriah-gw-01:/sci/backup/aerez/aerez/moshea/ncbi_mags$ srun sra-stat --meta --quick SRR2244401 srun: job 20797919 queued and waiting for resources srun: job 20797919 has been allocated resources 2024-01-10T13:10:32 sra-stat.3.0.10 int: directory not found while opening manager within virtual file system module - 'SRR2244401' srun: error: glacier-03: task 0: Exited with exit code 3

rvalieris commented 10 months ago

did you follow these steps to configure the toolkit ? https://github.com/ncbi/sra-tools/wiki/05.-Toolkit-Configuration

if it works without slurm, it might be because the config files are not visible in the node.