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Ecogenomics / CheckM

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
https://ecogenomics.github.io/CheckM/
GNU General Public License v3.0
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AttributeError: 'Namespace' object has no attribute 'bCalledGenes' #332

Closed neelam19051 closed 2 years ago

neelam19051 commented 2 years ago

Hi I am trying to make plot by using checkm output and the error is given below- Please help me if anyone know anything about it.

**checkm gc_plot ./bins ./plots 95

CheckM v1.1.9 [2022-04-21 17:12:06] INFO: checkm gc_plot ./bins ./plots 95 [2022-04-21 17:12:06] INFO: CheckM data: /home/bvs/anaconda3/envs/myenv/checkm_data [2022-04-21 17:12:06] INFO: [CheckM - gc_plot] Creating GC histogram and delta-GC plot.

Unexpected error: <class 'AttributeError'> Traceback (most recent call last): File "/home/bvs/anaconda3/envs/myenv/bin/checkm", line 856, in checkmParser.parseOptions(args) File "/home/bvs/anaconda3/envs/myenv/lib/python3.9/site-packages/checkm/main.py", line 996, in parseOptions self.gcPlot(options) File "/home/bvs/anaconda3/envs/myenv/lib/python3.9/site-packages/checkm/main.py", line 471, in gcPlot checkBinInputExists(options.bin_input, options.bCalledGenes) AttributeError: 'Namespace' object has no attribute 'bCalledGenes'

Thank you

donovan-h-parks commented 2 years ago

Hi. Thanks for pointing this out. The issue has been fixed in v1.1.10.

neelam19051 commented 2 years ago

Hi, could you please share checkm plot script in detail because even after updating still i am unable to plot.

Thank you

neelam19051 commented 2 years ago

Hi, could you please tell me where i am wrong ?

checkm gc_plot ./bins ./plots 90 [2022-04-22 11:07:52] INFO: CheckM v1.1.10 [2022-04-22 11:07:52] INFO: checkm gc_plot ./bins ./plots 90 [2022-04-22 11:07:52] INFO: CheckM data: /home/bvs/.checkm [2022-04-22 11:07:52] INFO: [CheckM - gc_plot] Creating GC histogram and delta-GC plot. [2022-04-22 11:07:52] ERROR: No bins found. Check the extension (-x) used to identify bins.

Controlled exit resulting from an unrecoverable error or warning.

Thank you!

donovan-h-parks commented 2 years ago

Hi,

If the FASTA files in your bins directory don't end in .fna you need to set the correct extension with the -x flag, e.g.:

> checkm gc_plot ./bins ./plots 90 -x .fa
neelam19051 commented 2 years ago

Hi, Thank you for your reply but still i am unable to plot even after providing fna file. Can check it again please.

checkm gc_plot /home/bvs/neelam/genome/fna_p ./plots 95 [2022-04-22 21:43:47] INFO: CheckM v1.1.10 [2022-04-22 21:43:47] INFO: checkm gc_plot /home/bvs/neelam/genome/fna_p ./plots 95 [2022-04-22 21:43:47] INFO: CheckM data: /home/bvs/.checkm [2022-04-22 21:43:47] INFO: [CheckM - gc_plot] Creating GC histogram and delta-GC plot. [2022-04-22 21:43:47] INFO: Plotting GC plots for /home/bvs/neelam/genome/fna_p/P_aeruginosa_1.fna (1 of 359) [2022-04-22 21:43:47] ERROR: Input file does not exists: /home/bvs/.checkm/distributions/gc_dist.txt

Controlled exit resulting from an unrecoverable error or warning.

Thank you

donovan-h-parks commented 2 years ago

Hi,

This is an installation issue. CheckM has reference data it needs to be able to locate: https://github.com/Ecogenomics/CheckM/wiki/Installation#required-reference-data

Cheers, Donovan

neelam19051 commented 2 years ago

Thank you so much for your help ..Now it solve.

neelam19051 commented 2 years ago

Hi, i am getting this error during marker plot, if possible please have a look. checkm marker_plot ./output /home/bvs/neelam/genome/fna_p ./plots_6 [2022-04-24 17:40:30] INFO: CheckM v1.1.10 [2022-04-24 17:40:30] INFO: checkm marker_plot ./output /home/bvs/neelam/genome/fna_p ./plots_6

Thank you! [2022-04-24 17:40:30] INFO: CheckM data: /home/bvs/neelam/checkm_data [2022-04-24 17:40:30] INFO: [CheckM - marker_plot] Creating marker gene position plot. [2022-04-24 17:40:38] INFO: Plotting marker gene position plot for P_aeruginosa_1 (1 of 359) [2022-04-24 17:40:38] INFO: Markers reside on 1 of 2 sequences which span 7.21 of 7.23 (99.7%) Mb

Unexpected error: <class 'AttributeError'> Traceback (most recent call last): File "/home/bvs/anaconda3/envs/myenv/bin/checkm", line 856, in checkmParser.parseOptions(args) File "/home/bvs/anaconda3/envs/myenv/lib/python3.9/site-packages/checkm/main.py", line 1009, in parseOptions self.markerPlot(options) File "/home/bvs/anaconda3/envs/myenv/lib/python3.9/site-packages/checkm/main.py", line 702, in markerPlot bPlotted = plot.plot(f, markerGeneStats[binId], binStats[binId]) File "/home/bvs/anaconda3/envs/myenv/lib/python3.9/site-packages/checkm/plot/markerGenePosPlot.py", line 112, in plot yLabelBounds = self.yLabelExtents(yLabels, self.options.font_size) File "/home/bvs/anaconda3/envs/myenv/lib/python3.9/site-packages/checkm/plot/AbstractPlot.py", line 124, in yLabelExtents bboxi = bbox.inverse_transformed(self.fig.transFigure) AttributeError: 'Bbox' object has no attribute 'inverse_transformed'

donovan-h-parks commented 2 years ago

Hi. This should be fixed in v1.1.11. Thanks.

neelam19051 commented 2 years ago

Hi, thank you so much, now it's working perfectly fine. could you please tell me how to make single plot for all large genome, however it plot single plot for single genome.

Thank you

donovan-h-parks commented 2 years ago

Hi. The marker_plot creates a single row per genome. It doesn't have the capability of producing any other style of plot.