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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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pVACseq is deprecated and it is now called pVACtools #21

Closed rezakj closed 1 year ago

rezakj commented 1 year ago

The pipeline went fine all the way until step number 12 and I got this error:

Do you think it's because the pVACseq is deprecated?

icbi/nextNEOpi execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 1. The full error message was: Error executing process > 'pVACseq (sample2)' Caused by: ProcesspVACseq (sample2)terminated with an error exit status (1) Command executed: pvacseq run \ --iedb-install-directory /opt/iedb \ -t 10 \ -p sample2_vep_phased.vcf.gz \ -e1 8,9,10,11 \ -e2 15,16,17,18,19,20,21,22,23,24,25 \ --normal-sample-name sample2_normal \ --tumor-purity 0.68 \ \ --netmhc-stab \ --binding-threshold 500 --top-score-metric median --minimum-fold-change 0.0 --normal-cov 5 --tdna-cov 10 --trna-cov 10 --normal-vaf 0.02 --tdna-vaf 0.25 --trna-vaf 0.25 --expn-val 1 --maximum-transcript-support-level 1 \ sample2_vep_somatic_gx.vcf.gz sample2_tumor HLA-B*27:02 NetMHCpan MHCflurry NetMHCIIpan ./

riederd commented 1 year ago

Thanks for your interest in nextNEOpi.

Can you post the .nextflow.log file?

rezakj commented 1 year ago

Thank you for the quick response.

I just saw the log file and it might have been because of the python load error, I fixed the error and will keep you updated after the second run. Here is the error:

Downloading nextflow dependencies. It may require a few seconds, please wait .. NOTE: Nextflow is not tested with Java 1.8.0_292 -- It's recommended the use of version 11 up to 18 (B Downloading nextflow dependencies. It may require a few seconds, please wait .. Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.UnsupportedClassVersionError: org/eclipse/jgit/api/errors/GitAPIException has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) at java.lang.Class.privateGetMethodRecursive(Class.java:3048) at java.lang.Class.getMethod0(Class.java:3018) at java.lang.Class.getMethod(Class.java:1784) at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:650) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:632) Loading python/cpu/2.7.15 ERROR: python/cpu/2.7.15 cannot be loaded due to a conflict. HINT: Might try "module unload miniconda3/gpu/4.9.2" first. Loading manta/1.6.0 ERROR: Load of requirement 'python/cpu/2.7.15' failed

rezakj commented 1 year ago

Issue solved. It was the python error I mentioned. Thank you for the work you for the pipline and the you have done!