search

epifluidlab / FinaleMe

MIT License
9 stars 1 forks source link

STEP1 ：Exception in thread "main" java.lang.IllegalArgumentException: Invalid reference index -1 #5

Closed pei-wang111 closed 4 months ago

pei-wang111 commented 4 months ago

Hi, I am trying to run your code. but I get an error in step 1: Exception in thread "main" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:365) at org.cchmc.epifluidlab.finaleme.utils.CpgMultiMetricsStats.doMain(CpgMultiMetricsStats.java:598) at org.cchmc.epifluidlab.finaleme.utils.CpgMultiMetricsStats.main(CpgMultiMetricsStats.java:144)

I run it with the following code: samtools sort -o BH01.chr22.sorted.bam BH01.chr22.bam samtools index BH01.chr22.sorted.bam java -Xmx20G -cp "target/FinaleMe-0.58-jar-with-dependencies.jar:lib/gatk-package-distribution-3.3.jar:lib/sis-jhdf5-batteries_included.jar:lib/java-genomics-io.jar:lib/igv.jar" org.cchmc.epifluidlab.finaleme.utils.CpgMultiMetricsStats files/hg19.2bit files/CG_motif.hg19.common_chr.pos_only.bedgraph files/CG_motif.hg19.common_chr.pos_only.bedgraph files/BH01.chr22.sorted.bam CpgMultiMetricsStats.hg19.details.bed.gz -stringentPaired -excludeRegions files/wgEncodeDukeMapabilityRegionsExcludable_wgEncodeDacMapabilityConsensusExcludable.hg19.bed -valueWigs methyPrior:0:files/wgbs_buffyCoat_jensen2015GB.methy.hg19.bw -wgsMode

wgEncodeDukeMapabilityRegionsExcludable_wgEncodeDacMapabilityConsensusExcludable.hg19.bed,wgbs_buffyCoat_jensen2015GB.methy.hg19.bw are provided in the tutorial. hg19.2bit downloaded from UCSC, the content of CG_motif.hg19.common_chr.pos_only.bedgraph file is as follows:

chr22 16122622 16122923 chr22 16155753 16158017 chr22 16192654 16193098 chr22 16200149 16200707 chr22 16217287 16217676 chr22 16228205 16228546 chr22 16288314 16288570 chr22 16374539 16374899 chr22 16404342 16404671 chr22 16423842 16424117 ......

Can you please help me?

pei-wang111 commented 4 months ago

I have resolved the issue already, still, thank you.