jonathancrabtree / Circleator

Flexible circular visualization of genome-associated data with BioPerl and SVG.
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Can't locate object method "get_values" of "Circleator::SeqFunction::BAMCoverage" #38

Closed michaelgruenstaeudl closed 5 years ago

michaelgruenstaeudl commented 5 years ago

Hi Jonathan, upon the installation of Circleator, I successfully generated executed all commands and, thus, generated all figures of the tutorial GenBank Flat File Visualization.

However, I cannot execute any of the commands of the tutorial Coverage Plots Using BAM Files. Already when attempting to execute the first command of Example 1, I receive the following error, despite samtools being properly accessible to Circleator.

$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.7-16-g5231e3b (using htslib 1.9)
Usage:   samtools <command> [options]
...

$ circleator --data=lambda_virus.fa --config=coverage-ex1.txt > coverage-ex1.svg
INFO - started drawing figure using coverage-ex1.txt
INFO - reading from annot_file=./lambda_virus.fa, seq_file=, with seqlen=
INFO - gi|9626243|ref|NC_001416.1|: 0 feature(s) and 48502 bp of sequence
INFO - read 1 contig(s) from 1 input annotation and/or sequence file(s)
Can't locate object method "get_values" via package "Circleator::SeqFunction::BAMCoverage" at /usr/share/perl5/site_perl/Circleator/Util/Graphs.pm line 57.

The most I can deduct myself is that something is wrong regarding the linking to, or the execution of, the function get_values of package Circleator::SeqFunction::BAMCoverage, which wraps around samtools to extract the mpileup coverage values.

Any idea of what this error may be due to? Thanks, Michael