search

stat-lab / EvalSVcallers

Evaluate the performances (precision and recall) of structural variation (SV) callers
32 stars 13 forks source link

Failed at merging genotype files #11

Closed Mkddb closed 3 years ago

Mkddb commented 3 years ago

Dear Team,

I am running available MELT v2.2.0 for MEI analysis on Real dataset 4 (SRR1910373).

used the following command to process the bam file :

java -Xmx2G -jar MELT.jar Preprocess -bamfile SRR1910373_sorted.bam -h hs37d5.fa

Got this result :

Command Line: MELT.jar Preprocess -bamfile SRR1910373_sorted.bam -h hs37d5.fa

Start time: Sep 22, 2020 11:11:20 AM

Performing MELT analysis... All BAM Reference sequences are present in the provided reference. Total reads processed: 617999255 Total proper pairs: 593813636 Supp reads filtered: 8645606 Percent discordant: 2.54 BAM has within the expected tolerance for improper pairs, safe to proceed with MELT analysis. End time: Sep 22, 2020 11:54:53 AM

But, when i am running it for any class of MEI, it's throwing me some error at merging genotype files step.

Command used : java -Xmx10G -jar MELT.jar Single -bamfile SRR1910373_sorted.bam -h hs37d5.fa -n /MELTv2.2.0/add_bed_files/1KGP_Hg19/hg19.genes.bed -t /MELTv2.2.0/me_refs/1KGP_Hg19/SVA_MELT.zip -w /Melt20092020/ -r 251 -e 681 -c 30

Getting this error : Merging all genotype calls and statistics into final VCF output. Current time: Sep 23, 2020 4:59:48 PM The following files appear to be shorter than expected. Please ensure that the genotyping step finished properly for all files, and that the total number of lines in each genotyping file matches the number of lines in the SVA.pre_geno.tsv file. SRR1910373_sorted.SVA.tsv Failed at merging genotype files, please see below for stack trace... Exiting!

-------------------JAVA STACK TRACE------------------- java.lang.Exception: Incorrect genotyping file sizes at MELT.MELTIllumina.mergeTSV.MergeTSV.CheckFileLengths(MergeTSV.java:428) at MELT.MELTIllumina.mergeTSV.MergeTSV.doWork(MergeTSV.java:202) at MELT.MELTIllumina.runtimes.StepFour.RunStepFour(StepFour.java:32) at MELT.MELTIllumina.runtimes.SingleGenome.RunSingleGenome(SingleGenome.java:88) at MELT.MELTImplement.main(MELTImplement.java:65) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

MELT version: 2.2.0 -------------------END STACK TRACE!-------------------

Though, i manually checked that both the .tsv files has equal number of entries in rows as 151 entries.

Can you please help me in troubleshooting ??