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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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Post Calculate Exon/Repeat Interactions error: 0 regions loaded from file #26

Closed synanth closed 1 year ago

synanth commented 1 year ago

Hi, I've been trying to run LIONS on some data and have run across the following issue: RegionsCoverageFromWigCalculator fails to run as chromosomal analysis is skipped because they haven't been included in the region file. It looks like its failing at chimericReadSearch.py.

synanth commented 1 year ago

`$Id: RegionsCoverageFromWigCalculator.java 82545 2012-08-09 04:05:11Z mbilenky $ Loading chromosome lengths from /mnt/beegfs/home/stexocaelum/li_lab/me_cfs/LIONS/resources/hg38/genome/hg38.chr.size Lengths for 455 chromosomes are loaded load /mnt/beegfs/home/stexocaelum/li_lab/me_cfs/LIONS/projects/me_cfs/me_cfs/tmp_uniq_repeat_coords 0 regions loaded from file Skipping analysis on chr 1 because this chr was not included in the region file

... (a whole bunch of the same)

Skipping analysis on chr KI270394.1 because this chr was not included in the region file Exception in thread "main" java.lang.NullPointerException: Cannot invoke "java.lang.Comparable.compareTo(Object)" because "k1" is null at java.base/java.util.TreeMap.compare(TreeMap.java:1569) at java.base/java.util.TreeMap.addEntryToEmptyMap(TreeMap.java:776) at java.base/java.util.TreeMap.put(TreeMap.java:785) at java.base/java.util.TreeMap.put(TreeMap.java:534) at java.base/java.util.TreeSet.add(TreeSet.java:255) at src.tools.RegionsCoverageFromWigCalculator.execute(RegionsCoverageFromWigCalculator.java:255) at src.tools.RegionsCoverageFromWigCalculator.main(RegionsCoverageFromWigCalculator.java:55)`

ababaian commented 1 year ago

@synanth Sorry I keep meaning ot get to this but have been swamped the last couple of weeks! My apologies.

Can I recommend trying ChimeraTE (https://www.biorxiv.org/content/10.1101/2022.09.05.505575v1.full) which is written by actual software developers. This program has very similar core functionality to LIONS, but it's probably 200% more usable.