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ValueError running StoatyDive #3

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Braulium opened this issue Mar 19, 2022 · 1 comment
Open

ValueError running StoatyDive #3

Braulium opened this issue Mar 19, 2022 · 1 comment

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@Braulium
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Dear StoatyDive team,

I am trying to run StoatyDive in a series of eCLIP datasets, but it seems there is some problem with the creation of the plots.

In stdout I get:
[START]
[NOTE] Activate Peak Correction
[NOTE] Maximal peak length 200.
[NOTE] Calculate Coverage
[NOTE] 391726 peaks will be evaluated.
[NOTE] Activate border penalty.
[NOTE] 85033 peaks are covered.
[NOTE] Generate CV plot.

And in stderr I get the following error:
***** WARNING: File ../4_demultiplexed_umi/CLIP_OB1_Aligned.out_sorted.rmDup.bam has inconsistent naming convention for record:
GL456210.1 41175 41210 NS500318:1064:H5MG5BGXL:4:11503:11556:4102_GTCACAGAAA 255 -

***** WARNING: File ../4_demultiplexed_umi/CLIP_OB1_Aligned.out_sorted.rmDup.bam has inconsistent naming convention for record:
GL456210.1 41175 41210 NS500318:1064:H5MG5BGXL:4:11503:11556:4102_GTCACAGAAA 255 -

***** WARNING: File ../4_demultiplexed_umi/CLIP_OB1_Aligned.out_sorted.rmDup.bam has inconsistent naming convention for record:
GL456210.1 41175 41210 NS500318:1064:H5MG5BGXL:4:11503:11556:4102_GTCACAGAAA 255 -

***** WARNING: File ../4_demultiplexed_umi/CLIP_OB1_Aligned.out_sorted.rmDup.bam has inconsistent naming convention for record:
GL456210.1 41175 41210 NS500318:1064:H5MG5BGXL:4:11503:11556:4102_GTCACAGAAA 255 -

Traceback (most recent call last):
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/bin/StoatyDive.py", line 4, in
import('pkg_resources').run_script('StoatyDive==1.0.4', 'StoatyDive.py')
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/pkg_resources/init.py", line 662, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/pkg_resources/init.py", line 1459, in run_script
exec(code, namespace, namespace)
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/StoatyDive-1.0.4-py3.10.egg/EGG-INFO/scripts/StoatyDive.py", line 636, in
main()
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/StoatyDive-1.0.4-py3.10.egg/EGG-INFO/scripts/StoatyDive.py", line 553, in main
plt.xticks([], 'none')
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/matplotlib/pyplot.py", line 1795, in xticks
labels = ax.set_xticklabels(labels, **kwargs)
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/matplotlib/axes/_base.py", line 75, in wrapper
return get_method(self)(*args, **kwargs)
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/matplotlib/axis.py", line 1798, in _set_ticklabels
return self.set_ticklabels(labels, minor=minor, **kwargs)
File "/scicore/home/scheiffe/ortiz0000/anaconda3/envs/stoatydive/lib/python3.10/site-packages/matplotlib/axis.py", line 1720, in set_ticklabels
raise ValueError(
ValueError: The number of FixedLocator locations (0), usually from a call to set_ticks, does not match the number of ticklabels (4).

For the warnings, I have check and the chromosomal names match between the Bam files and the chrom.sizes file.
For the ValueError raised, I have no idea what can be the origin of the issue. I check the formating of my bed6 input files and everything seems to be correct there.

Thanks!

@heylf
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heylf commented Jun 21, 2022

Fixed. Currenlty the dev branch holds the hotfix.

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