Exception in thread "main" java.lang.NoClassDefFoundError

[topherconley]

Here is the command I ran:

$SAMTOOLS sort -m 5G -n -@ 5 ${OUT}.bam | \
    java -Xmx16G -jar $QORTS QC \
    --nameSorted \
    --stranded \
    --title $OUT \
    - \
    $GTF ./

Attached is the log output. The same command worked on other similar paired-end files.
qorts.txt

Any thoughts?
Chris

[hartleys]

That's a new one. What's the java version? Also, have you tried not running it in a pipe? Just for testing purposes.

…

On Fri, Jun 29, 2018, 11:32 AM Chris Conley ***@***.***> wrote: Here is the command I ran: $SAMTOOLS sort -m 5G -n -@ 5 ${OUT}.bam | \ java -Xmx16G -jar $QORTS QC \ --nameSorted \ --stranded \ --title $OUT \ - \ $GTF ./ Attached is the log output. The same command worked on other similar paired-end files. qorts.txt <https://github.com/hartleys/QoRTs/files/2149958/qorts.txt> Any thoughts? Chris — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#65>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwu7I06KH2U-XZIJIgv1pS2-UFYu6Xlks5uBkhygaJpZM4U9N9F> .