JAVA ERROR RUNNING VARDICTJAVA

[espelpz]

Hi,

I tried running VarDict to get somatic variants but it was too slow, so I am trying to run VarDictJava. I am not able to make it work, everytime I try to run VarDictJava I get this kind of error message:

WARNING: BAM index file CASO_002_1.bai is older than BAM CASO_002_1.bam

WARNING: BAM index file CASO_002_1.bai is older than BAM CASO_002_1.bam
There was Exception while processing position on 55270347 on region chr7:55270300-55270348. The processing will be continued from the next position.
java.lang.NumberFormatException: For input string: "38,0"
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.base/java.lang.Double.parseDouble(Double.java:543)
at com.astrazeneca.vardict.Utils.roundHalfEven(Utils.java:102)
at com.astrazeneca.vardict.modules.ToVarsBuilder.createVariant(ToVarsBuilder.java:442)
at com.astrazeneca.vardict.modules.ToVarsBuilder.process(ToVarsBuilder.java:144)
at java.base/java.util.concurrent.CompletableFuture.uniApplyNow(CompletableFuture.java:680)
at java.base/java.util.concurrent.CompletableFuture.uniApplyStage(CompletableFuture.java:658)
at java.base/java.util.concurrent.CompletableFuture.thenApply(CompletableFuture.java:2094)
at com.astrazeneca.vardict.modes.AbstractMode.pipeline(AbstractMode.java:51)
at com.astrazeneca.vardict.modes.SomaticMode.processBothBamsInPipeline(SomaticMode.java:111)
at com.astrazeneca.vardict.modes.SomaticMode.notParallel(SomaticMode.java:49)
at com.astrazeneca.vardict.VarDictLauncher.start(VarDict

VarDictJava fails (there were 11 continued exceptions during the run).
Critical exception occurs on region: chr7:55270300-55270348, program will be stopped.
java.util.concurrent.CompletionException: java.lang.RuntimeException: java.lang.NumberFormatException: For input string: "40,0"
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:314)
at java.base/java.util.concurrent.CompletableFuture.uniApplyNow(CompletableFuture.java:683)
at java.base/java.util.concurrent.CompletableFuture.uniApplyStage(CompletableFuture.java:658)
at java.base/java.util.concurrent.CompletableFuture.thenApply(CompletableFuture.java:2094)
at com.astrazeneca.vardict.modes.AbstractMode.pipeline(AbstractMode.java:51)
at com.astrazeneca.vardict.modes.SomaticMode.processBothBamsInPipeline(SomaticMode.java:111)
at com.astrazeneca.vardict.modes.SomaticMode.notParallel(SomaticMode.java:49)
at com.astrazeneca.vardict.VarDictLauncher.start(VarDictLauncher.java:65)
at com.astrazeneca.vardict.Main.main(Main.java:15)
Caused by: java.lang.RuntimeException: java.lang.NumberFormatException: For input string: "40,0"
at com.astrazeneca.vardict.Utils.printExceptionAndContinue(Utils.java:276)
at com.astrazeneca.vardict.modules.ToVarsBuilder.process(ToVarsBuilder.java:164)
at java.base/java.util.concurrent.CompletableFuture.uniApplyNow(CompletableFuture.java:680)
... 7 more
Caused by: java.lang.NumberFormatException: For input string: "40,0"
at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.base/java.lang.Double.parseDouble(Double.java:543)
at com.astrazeneca.vardict.Utils.roundHalfEven(Utils.java:102)
at com.astrazeneca.vardict.modules.ToVarsBuilder.createVariant(ToVarsBuilder.java:442)
at com.astrazeneca.vardict.modules.ToVarsBuilder.process(ToVarsBuilder.java:144)
... 8 more

How could I solve this issue?

I am pasting the command run down below:

/home/espell/Programas/VarDictJava/build/install/VarDict/bin/VarDict -G /home/espell/Proyectos/referencias/GRCh38/GRCh38_aws-igenomes/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta -f 0.01 -N 1_CASO_002 -b "CASO_002_1.bam|CASO_002_0.bam" -R chr7:55270300-55270348:EGFR

Thank you in advance!