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Questions about installation and output #60

Closed lachlansimpson closed 6 years ago

lachlansimpson commented 6 years ago

I seem to have successfully installed. Running make give a couple of

warning: comparison between signed and unsigned integer expressions [-Wsign-compare] │bamliquidator_batch.py bamPlot.py bamPlot_turbo.R bamToGFF.py if (columns.size() > name_column)

errors, but otherwise finishes without error and re-running make gives "nothing to be done for all".

When I then run the python bamliquidatorbatch/test.py I get a list of errors, but it also seems to finish OK?

(c2c4865)[root@vmpr-res-utils bamliquidator_internal]# python bamliquidatorbatch/test.py 
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
/config/binaries/bamliquidator/c2c4865/pipeline/bamliquidator_internal/bamliquidatorbatch/normalize_plot_and_summarize.py:245: RuntimeWarning: invalid value encountered in true_divide
  percentiles = (stats.rankdata(normalized_count_list) - 1) / (len(normalized_count_list)-1) * 100
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: bb196b99-4a58-4101-9e42-fa6e85dcf111
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: 0077eb96-20e6-42d8-a1e8-374225a7b234
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: a3f49d52-d8f1-46e1-a917-6354df750de3
.[samopen] SAM header is present: 1 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: f2820684-62a3-4545-aaa9-f26aaffb4853
.[samopen] SAM header is present: 1 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: f9a53df4-88ef-451e-9d3e-c4a3a7273bc0
.[samopen] SAM header is present: 2 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: 71a41d72-cd89-4910-9b59-be73ce4b3784
.[samopen] SAM header is present: 3 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: e4151f76-757a-470e-8477-b0da65e657b3
.[samopen] SAM header is present: 3 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: 9f0e6d71-a4d8-4e71-adc4-efbf6fdc5337
.[samopen] SAM header is present: 1 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: d5ef915b-02cf-4018-900f-c848789f892e
.[samopen] SAM header is present: 1 sequences.
ERROR   Bin size cannot be zero
.[samopen] SAM header is present: 1 sequences.
ERROR:/config/binaries/bamliquidator/c2c4865/lib/python2.7/site-packages/bokeh/validation/check.pyc:W-1002 (EMPTY_LAYOUT): Layout has no children: VBox, ViewModel:VBox, ref _id: 28b0a72b-b8c5-464a-880e-32c0248d5e2d
.[samopen] SAM header is present: 1 sequences.
WARNING No valid regions detected in /tmp/blt_JBCZN1/empty.gff
WARNING No valid regions detected in /tmp/blt_JBCZN1/empty.gff
.[samopen] SAM header is present: 1 sequences.
WARNING Excluding invalid region on line 1: bam file key 1 chr1 region1 60 -> 70 . 0
WARNING No valid regions detected in /tmp/blt_tc4K9_/single.gff
.[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
ERROR   Unhandled exception: Not enough columns parsing line 1 '' of /tmp/blt_kEPPRo/single.bed
ERROR   Unhandled exception: Not enough columns parsing line 1 'chr1' of /tmp/blt_kEPPRo/single.bed
ERROR   Unhandled exception: Not enough columns parsing line 1 'chr1    1' of /tmp/blt_kEPPRo/single.bed
.[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
WARNING Truncated region on line 1 from 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr' to 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr'
.[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
WARNING Truncated region on line 1 from 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr' to 'rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrr'
.[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
.[samopen] SAM header is present: 1 sequences.
WARNING Excluding invalid region on line 1: bam file key 1 chr10 region1 60 -> 70 . 0
WARNING No valid regions detected in /tmp/blt_oG3vu5/single.gff
.
----------------------------------------------------------------------
Ran 22 tests in 2.447s

OK
Closing remaining open files:/tmp/blt_ByyONM/output/counts.h5...done

Is that what I should be expecting?

jdimatteo commented 6 years ago

Yes, the final OK is what you should expect. You can ignore the previous warnings