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schmeing / gapless

Gapless provides combined scaffolding, gap-closing and assembly correction with long reads
MIT License
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pipeline crashed : scaffold (unexpected keyword argument 'nonpositive') #7

Open DiegoSafian opened 1 year ago

DiegoSafian commented 1 year ago

Hi,

I have run the pipeline but i crashed in the first run.

This is my script:

gapless.sh -j 32 -i genome.fa \
            -t nanopore prome_filtered.fastq \
            -n 3 \
            -o ./gapless

I have attached all the .log files. Could you please help me with this.

gapless_scaffold.log gapless_split.log minimap2_reads.log minimap2_repeats.log

schmeing commented 1 year ago

Hi,

Thank you for reporting this issue. I checked the recent documentation of matplotlib and ax.set_yscale('log', nonpositive='clip') is still the recommended way of setting the log scale: https://matplotlib.org/stable/api/scale_api.html https://matplotlib.org/stable/gallery/scales/log_demo.html#sphx-glr-gallery-scales-log-demo-py

So, for me it would be important to understand if this is something about the library versions imported or something dataspecific. Could you open a python console from the same environment you use to run gapless and run this:

from matplotlib import use as mpl_use
mpl_use('Agg')
import seaborn as sns

ax = sns.distplot([4,7,8,3,2,7,9,5,3,7,8,2,1,9], bins=2, kde=False, color='w')
ax.set_yscale('log', nonpositive='clip')

If you get the same error: How did you install gapless? In case you used conda, can you provide me with the command you used to set it up, please? In case you do not use conda, could you try conda, please?

In case you do not get an error, could you try subsetting mappings['mapq'] in the following line:

PlotHist(pdf, "Mapping quality", "# Mappings", mappings['mapq'], threshold=min_mapq, logy=True)

to the smallest subset that still has this error and share this subset with me, please?