search

epifluidlab / FinaleMe

MIT License
9 stars 1 forks source link

error Exception in thread "main" java.lang.IllegalArgumentException: Invalid reference index -1 #8

Open mxyoyeme opened 3 months ago

mxyoyeme commented 3 months ago

Hello, it is great work.

However, I encontered error in the very first step following your tutorial.

The script I was using is shown below:

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 hg19.2bit CG_motif.hg19.common_chr.pos_only.bedgraph CG_motif.hg19.common_chr.pos_only.bedgraph BH01.chr22.bam CpgMultiMetricsStats.hg19.details.bed.gz -stringentPaired -excludeRegions wgEncodeDukeMapabilityRegionsExcludable_wgEncodeDacMapabilityConsensusExcludable.hg19.bed -valueWigs methyPrior:0:wgbs_buffyCoat_jensen2015GB.methy.hg19.bw -wgsMode

The error message is shown below:

SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/mnt/d/cfDNA.zn/FinaleMe/target/FinaleMe-0.58-jar-with-dependencies.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/mnt/d/cfDNA.zn/FinaleMe/lib/gatk-package-distribution-3.3.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.apache.logging.slf4j.Log4jLoggerFactory] INFO [2024-06-11 16:50:29,633] [CpgMultiMetricsStats.java:192] [main] Processing interval file ... INFO [2024-06-11 16:50:29,657] [CpgMultiMetricsStats.java:199] [main] Excluding intervals ... INFO [2024-06-11 16:50:29,666] [CpgMultiMetricsStats.java:407] [main] Loading value interval big wig file ... INFO [2024-06-11 16:50:29,721] [CpgMultiMetricsStats.java:437] [main] Automate generate all k-mer until length 0 INFO [2024-06-11 16:50:29,721] [CpgMultiMetricsStats.java:482] [main] Loading CpG interval file ... INFO [2024-06-11 16:50:44,803] [CpgMultiMetricsStats.java:536] [main] Get total reads number used for scaling from bam file... INFO [2024-06-11 16:51:15,272] [CpgMultiMetricsStats.java:554] [main] 27006990 reads in total ... INFO [2024-06-11 16:51:15,272] [CpgMultiMetricsStats.java:556] [main] Output value for each CpG in each DNA fragment ... 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)

Any advice?

Thanks a lot!

TongZhou202103 commented 1 month ago

I have the same problem as you!!!! Have you solved it?

mxyoyeme commented 4 days ago

I have the same problem as you!!!! Have you solved it?

No. Did you?