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`--quiet` flag does not work for prefetch #894

Closed amstilp closed 5 months ago

amstilp commented 5 months ago

Passing the --quiet flag to prefetch does nothing. From the help, I would expect it to print nothing (or very little) to standard out.

With the quiet flag:

$ /projects/resources/software/apps_ubuntu/sratoolkit.3.0.2-ubuntu64/bin/prefetch --quiet --cart cart_DAR117119_202401111357.krt --ngc /projects/primed/dbgap/prj_33119_D13875.ngc
Downloading kart file 'cart_DAR117119_202401111357.krt'
Checking sizes of kart files...

2024-01-11T22:53:18 prefetch.3.0.2: Current preference is set to retrieve SRA Lite files with simplified base quality scores.
2024-01-11T22:53:19 prefetch.3.0.2: Current preference is set to retrieve SRA Lite files with simplified base quality scores.

Downloading the files...

2024-01-11T22:53:19 prefetch.3.0.2: 1) Downloading 'phs000007.v33.pht003310.v6.p14.t_echocs_ex08_1_0705s.var_report.xml'...
2024-01-11T22:53:19 prefetch.3.0.2:  Downloading via HTTPS...
2024-01-11T22:53:20 prefetch.3.0.2:  HTTPS download succeed
2024-01-11T22:53:20 prefetch.3.0.2: 1) 'phs000007.v33.pht003310.v6.p14.t_echocs_ex08_1_0705s.var_report.xml' was downloaded successfully
2024-01-11T22:53:20 prefetch.3.0.2: 2) Downloading 'phs000007.v33.pht006007.v1.e_exam_ex31_0_0738s.data_dict.xml'...
2024-01-11T22:53:20 prefetch.3.0.2:  Downloading via HTTPS...
2024-01-11T22:53:21 prefetch.3.0.2:  HTTPS download succeed
2024-01-11T22:53:21 prefetch.3.0.2: 2) 'phs000007.v33.pht006007.v1.e_exam_ex31_0_0738s.data_dict.xml' was downloaded successfully

Without the quiet flag:

$ /projects/resources/software/apps_ubuntu/sratoolkit.3.0.2-ubuntu64/bin/prefetch --cart cart_DAR117119_202401111357.krt --ngc /projects/primed/dbgap/prj_33119_D13875.ngc ; rm phs*
Downloading kart file 'cart_DAR117119_202401111357.krt'
Checking sizes of kart files...

2024-01-11T22:54:19 prefetch.3.0.2: Current preference is set to retrieve SRA Lite files with simplified base quality scores.
2024-01-11T22:54:21 prefetch.3.0.2: Current preference is set to retrieve SRA Lite files with simplified base quality scores.

Downloading the files...

2024-01-11T22:54:22 prefetch.3.0.2: 1) Downloading 'phs000007.v33.pht003310.v6.p14.t_echocs_ex08_1_0705s.var_report.xml'...
2024-01-11T22:54:22 prefetch.3.0.2:  Downloading via HTTPS...
2024-01-11T22:54:23 prefetch.3.0.2:  HTTPS download succeed
2024-01-11T22:54:23 prefetch.3.0.2: 1) 'phs000007.v33.pht003310.v6.p14.t_echocs_ex08_1_0705s.var_report.xml' was downloaded successfully
2024-01-11T22:54:23 prefetch.3.0.2: 2) Downloading 'phs000007.v33.pht006007.v1.e_exam_ex31_0_0738s.data_dict.xml'...
2024-01-11T22:54:23 prefetch.3.0.2:  Downloading via HTTPS...
2024-01-11T22:54:24 prefetch.3.0.2:  HTTPS download succeed
2024-01-11T22:54:24 prefetch.3.0.2: 2) 'phs000007.v33.pht006007.v1.e_exam_ex31_0_0738s.data_dict.xml' was downloaded successfully

There is no difference between the two outputs.

The help for prefetch says that --quiet is an option:

$ /projects/resources/software/apps_ubuntu/sratoolkit.3.0.2-ubuntu64/bin/prefetch --help
Usage:
  prefetch [options] <SRA accession> [...]
  Download SRA files and their dependencies

  prefetch [options] --cart <kart file>
  Download cart file
...
...
  -q|--quiet                       Turn off all status messages for the 
                                   program. Negated by verbose. 
...
...
durbrow commented 5 months ago

All of the tools in the toolkit accept --quiet and --verbose, but not all tools implement those options equally.

klymenko commented 1 month ago

@amstilp , we fixed response to --quiet in our 3.1.1 release.