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Formatting of the stdout text #8

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jakeb1996 opened this issue Feb 17, 2022 · 0 comments · May be fixed by #21
Open

Formatting of the stdout text #8

jakeb1996 opened this issue Feb 17, 2022 · 0 comments · May be fixed by #21

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@jakeb1996
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Some of the stdout log is inconsistently formatted, or is incorrect. See examples below.

There are several cases where large numbers are displayed with , separating 1000's. There are some cases where no ,'s are used.

>>> 2022-02-17 16:14:29:442676: Done.

>>> 2022-02-17 16:14:29:442723: 2500000 guides evaluated.

>>> 2022-02-17 16:14:29:442841: This batch ran in 01 00:40:21 (dd hh:mm:ss) or 2421.1502072811127 seconds

>>> 2022-02-17 16:14:29:442913: Processing batch file 2 of 7

>>> 2022-02-17 16:14:35:888107:         Loaded 2,500,000 guides

>>> 2022-02-17 16:14:35:888266: CHOPCHOP - remove those without G in position 20.

>>> 2022-02-17 16:15:13:670180:         773,162 of 1,043,323 failed here.

...

In the run that produced this output, the batch size was set to 2.5m guides, yet, below, on the second line, it says the page will contain 5m guides.
The page size would not be larger than the batch size.
I believe pageSize = min(batchSize, maxPageSize, actualPageSize) would be more accurate.
Also, notice the lack of commas again.


>>> 2022-02-17 16:17:10:869049: mm10db - check secondary structure.

>>> 2022-02-17 16:17:49:964502:         Processing page 1 (5,000,000 per page).

>>> 2022-02-17 16:17:49:964671:                 Constructing the RNAfold input file.

>>> 2022-02-17 16:17:50:481058:                 678,423 guides in this page.
...

>>> 2022-02-17 16:24:15:592360: Calculating mm10db final result.

>>> 2022-02-17 16:24:18:294110:         426284 accepted.

>>> 2022-02-17 16:24:18:294204:         2073716 failed.
jakeb1996 added a commit that referenced this issue Jan 11, 2024
@jakeb1996
fixed issues report in #8
cacfbfc
@jakeb1996 jakeb1996 linked a pull request Jan 11, 2024 that will close this issue
fixed issues report in #8 #21
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fixed issues report in #8 bmds-lab/Crackling
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@jakeb1996