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rvalieris / parallel-fastq-dump

parallel fastq-dump wrapper
MIT License
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query unauthorized while resolving query within virtual file #23

Closed Kapeel closed 4 years ago

Kapeel commented 4 years ago

Hi,

I installed parallel-fastq-dump on centos cluster using conda. I get the below error when I ran the example command.

$ which sra-stat.2.9.6 ~/.conda/envs/parallel-fastq-dump/bin/sra-stat.2.9.6

Error:

2019-08-15T20:36:57 sra-stat.2.9.6 err: query unauthorized while resolving query within virtual file 
system module - failed to resolve accession 'SRR1219899' - Access denied - please request permission 
to access phs000710/UR in dbGaP ( 403 )
2019-08-15T20:36:57 sra-stat.2.9.6 int: directory not found while opening manager within virtual file
 system module - 'SRR1219899'
SRR ids: ['SRR1219899']
extra args: ['--split-files', '--gzip']
tempdir: /tmp/uge/61368154.1.secondary.q/pfd_do4anflw
Traceback (most recent call last):
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/bin/parallel-fastq-dump", li
ne 4, in <module>
    __import__('pkg_resources').run_script('parallel-fastq-dump==0.6.5', 'parallel-fastq-dump')
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/lib/python3.7/site-packages/
pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/lib/python3.7/site-packages/
pkg_resources/__init__.py", line 1460, in run_script
    exec(script_code, namespace, namespace)
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/lib/python3.7/site-packages/
parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 112, in <module>
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/lib/python3.7/site-packages/
parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 105, in main
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/lib/python3.7/site-packages/
parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 15, in pfd
  File "/sonas-hs/ware/hpc/home/kchougul/.conda/envs/parallel-fastq-dump/lib/python3.7/site-packages/
parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 64, in get_spot_count
IndexError: list index out of range

Thanks

rvalieris commented 4 years ago

system module - failed to resolve accession 'SRR1219899' - Access denied - please request permission to access phs000710/UR in dbGaP ( 403 )

SRR1219899 is part of the 1000 Genomes Used for Cloud Testing dataset.

its a test dataset used to test pipelines that need dbGaP data (which needs special access). you can get access to this dataset by following the Protected Data Usage Guide

note that this is only for dbGaP protected data, if the data you want to download is public you don't need to do any of this.

nick-youngblut commented 4 years ago

I'm getting a similar IndexError, but no "failed to resolve accession":

2019-09-28T10:51:22 sra-stat.2.8.2 int: directory not found while opening manager within virtual file
 system module - '4563773.3'
SRR ids: ['4563773.3']
extra args: ['--skip-technical', '--split-3']
tempdir: /tmp/global/nyoungblut/LLMGQC_27982106400/parallel-fastq-dump_TMP_4563773.3/pfd_b6cr1k0j
Traceback (most recent call last):
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/bin/parallel-fastq-dump", l
ine 4, in <module>
    __import__('pkg_resources').run_script('parallel-fastq-dump==0.6.5', 'parallel-fastq-dump')
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/lib/python3.7/site-packages
/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/lib/python3.7/site-packages
/pkg_resources/__init__.py", line 1469, in run_script
    exec(script_code, namespace, namespace)
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/lib/python3.7/site-packages
/parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 112, in <module>
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/lib/python3.7/site-packages
/parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 105, in main
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/lib/python3.7/site-packages
/parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 15, in pfd
  File "/ebio/abt3_projects/software/dev/llmgqc/.snakemake/conda/03574a6a/lib/python3.7/site-packages
/parallel_fastq_dump-0.6.5-py3.7.egg/EGG-INFO/scripts/parallel-fastq-dump", line 64, in get_spot_coun
t
IndexError: list index out of range
rvalieris commented 4 years ago

@nick-youngblut thats different, it failed because 4563773.3 is not a valid SRA ID. run IDs usually begin with SRR or ERR.