Issue with Varscan modify about somaticseq HOT 13 CLOSED

Hi I tried with python3.6 (instead of python3.2) with the corresponding dependencies and consolidated the calls.
I ran the r scripts to train and predict on my own and they work as well. thanks

from somaticseq.

What was the file name of your VarScan's VCF file?

from somaticseq.

from somaticseq.

Is it possible that you send me the vcf.gz file so I can check?
I'm also wondering if Python 3.2.3's gzip library isn't somehow different from later versions.

Also, can you run docker on your end?
If so, we've just dockerized SomaticSeq: https://hub.docker.com/r/lethalfang/somaticseq/

from somaticseq.

Actually, why don't you unpack the bgzip'ed VCF file, and see if that fixes your problem.

from somaticseq.

from somaticseq.

from somaticseq.

The script uses GATK to combine all the VCF files from different callers (i.e., GATK CombineVariants).
You can point to the location of the GATK.jar file by --gatk $PATH/TO/GATK/GenomeAnalysis.jar

Alternatively, you can download the latest version 2.2.5. There, without --gatk, it'll just use cat and the vcfsorter.pl script to combine and sort those VCF files.

from somaticseq.

I provided the path to --gatk but it returned with this error:

Picked up _JAVA_OPTIONS: -XX:+UseSerialGC

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version 2.0-39-gd091f72):

ERROR The invalid arguments or inputs must be corrected before the GATK can proceed

ERROR Please do not post this error to the GATK forum

ERROR

ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Invalid command line: Failed to parse value null for argument referenceFile. This is most commonly caused by providing an incorrect data type (e.g. a double when an int is required)

ERROR ------------------------------------------------------------------------------------------

from somaticseq.

I have not tried GATK version 2 before.
Can you give GATK3 a try?
GATK4 beta doesn't work for now.

from somaticseq.

Trying with GATK3.7:

Picked up _JAVA_OPTIONS: -XX:+UseSerialGC
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

from somaticseq.

any specific GATK version to use?

from somaticseq.

I've tried most versions of GATK 3, including 3.7 and hasn't had a problem so far.
To get a detailed description of how each step in the script works, the documentation is in the docs folder:
https://github.com/bioinform/somaticseq/blob/master/docs/Manual.pdf

Starting from page 4 is the step-by-step guide of the pipeline.

from somaticseq.