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o-william-white / circos_plot_organelle

Python wrapper script to create an annotated circos plot.
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issues running program #5

Open AntonioBaeza opened 21 hours ago

AntonioBaeza commented 21 hours ago

When running the example, I also get errors:

(circos_plot_organelle) ant@hillary:~/circos_plot_organelle$ python circos_plot_organelle.py \

--fasta example_data/010210013_StH_H3.fasta --bam example_data/010210013_StH_H3.bam --bed example_data/010210013_StH_H3.bed --window 50 Running samtools coverage Calculating mean coverage in 50 bp windows Calculating GC content in 50 bp windows Running trf

Tandem Repeats Finder, Version 4.09 Copyright (C) Dr. Gary Benson 1999-2012. All rights reserved.

Loading sequence... Allocating Memory... Initializing data structures... Computing TR Model Statistics... Scanning... .....................

Freeing Memory... Resolving output... Done.

Finished trf Calculating N content in 50 bp windows Writing karyotype.txt Writing ideogram.conf Writing ticks.conf Writing circos.conf Writing annotations lables and gene files Running circos

REQUIRED MODULE(S) MISSING OR OUT-OF-DATE

You are missing one or more Perl modules, require newer versions, or some modules failed to load. Use CPAN to install it as described in this tutorial

http://www.circos.ca/documentation/tutorials/configuration/perl_and_modules

missing GD error Can't locate GD.pm in @inc (you may need to install the GD module) (@inc contains: /home/ant/miniconda3/envs/circos_plot_organelle/bin/lib /home/ant/miniconda3/envs/circos_plot_organelle/bin/../lib /home/ant/miniconda3/envs/circos_plot_organelle/bin /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/5.32/site_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/site_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/5.32/vendor_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/vendor_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/5.32/core_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/core_perl .) at (eval 39) line 1. missing GD::Polyline error Can't locate GD/Polyline.pm in @inc (you may need to install the GD::Polyline module) (@inc contains: /home/ant/miniconda3/envs/circos_plot_organelle/bin/lib /home/ant/miniconda3/envs/circos_plot_organelle/bin/../lib /home/ant/miniconda3/envs/circos_plot_organelle/bin /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/5.32/site_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/site_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/5.32/vendor_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/vendor_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/5.32/core_perl /home/ant/miniconda3/envs/circos_plot_organelle/lib/perl5/core_perl .) at (eval 40) line 1.

Finished circos Complete! (circos_plot_organelle) ant@hillary:/circos_plot_organelle$ ll total 8664 drwxrwxr-x 5 ant ant 4096 Nov 19 09:19 ./ drwxr-xr-x 77 ant ant 4096 Nov 19 09:06 ../ -rw-rw-r-- 1 ant ant 1359 Nov 19 09:19 010210013_StH_H3.fasta.2.7.7.80.10.50.500.dat -rw-rw-r-- 1 ant ant 16186 Nov 19 09:19 010210013_StH_H3.fasta.2.7.7.80.10.50.500.mask -rw-rw-r-- 1 ant ant 921 Nov 19 09:19 circos.conf -rw-rw-r-- 1 ant ant 7163 Nov 19 09:06 circos_plot_organelle.py drwxrwxr-x 2 ant ant 141 Nov 19 09:19 data/ drwxrwxr-x 2 ant ant 130 Nov 19 09:06 example_data/ -rw-rw-r-- 1 ant ant 8787718 Nov 18 21:35 fastpuncseqsMITOmapped.bam drwxrwxr-x 8 ant ant 4096 Nov 19 09:06 .git/ -rw-rw-r-- 1 ant ant 412 Nov 19 09:19 ideogram.conf -rw-rw-r-- 1 ant ant 15557 Sep 26 17:11 Jasus_frontalis.fasta -rw-rw-r-- 1 ant ant 1589 Nov 18 21:59 JfrontalisBEDmodified.bed -rw-rw-r-- 1 ant ant 59 Nov 19 09:19 karyotype.txt -rw-rw-r-- 1 ant ant 978 Nov 19 09:06 README.md -rw-rw-r-- 1 ant ant 437 Nov 19 09:19 ticks.conf (circos_plot_organelle) ant@hillary:/circos_plot_organelle$ (circos_plot_organelle) ant@hillary:~/circos_plot_organelle$