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ukhsa-collaboration / snapperdb

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Trying to run fastq to db. #23

Open DolapoA opened 5 years ago

DolapoA commented 5 years ago

I attempted to convert fastq to database as so but I came across the following error: I can't quite make out what exactly the cause is, I was wondering whether anyone has come across this as I don't really know where to go from here.

python run_snapperdb.py fastq_to_db -c ebg1_config.txt /path/file1-18_R1.fastq.gz /path/file-18_R2.fastq.gz Namespace(command='fastq_to_db', config_file='ebg1_config.txt', fastqs=['/path/file1-18_R1.fastq.gz ', '/path/file-18_R2.fastq.gz '], force='N', log_dir='/opt/snapperdb') [2019-01-09 09:40:26,274] INFO: Version: 1-4 [2019-01-09 09:40:26,274] INFO: Initialising data matrix. [2019-01-09 09:40:26,289] INFO: Mapping data file with bwa. [2019-01-09 09:43:35,351] INFO: Creating digitised variants with gatk. [2019-01-09 09:43:42,999] WARNING: Calling variants returned non-zero exit status. [2019-01-09 09:43:42,999] WARNING: Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/spark/Partitioner at java.lang.Class.getDeclaredConstructors0(Native Method) at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671) at java.lang.Class.getConstructors(Class.java:1651) at org.broadinstitute.hellbender.utils.ClassUtils.canMakeInstances(ClassUtils.java:30) at org.broadinstitute.hellbender.Main.extractCommandLineProgram(Main.java:317) at org.broadinstitute.hellbender.Main.setupConfigAndExtractProgram(Main.java:179) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:201) at org.broadinstitute.hellbender.Main.main(Main.java:288) Caused by: java.lang.ClassNotFoundException: org.apache.spark.Partitioner at java.net.URLClassLoader.findClass(URLClassLoader.java:382) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 8 more

[2019-01-09 09:43:42,999] ERROR: VCF was not created. path/file1-18_R1.filtered.vcf not found ...

This is what my log contains:

2019-01-16 11:54:10,228 snapperdb.fastq_to_vcf INFO PARAMS: config = ebg1_config.txt; fastqs = ['path/file2-16_R1.fastq.$ 2019-01-16 11:54:10,229 snapperdb.fastq_to_vcf INFO Running fastq_to_vcf 2019-01-16 11:54:10,229 snapperdb.fastq_to_vcf INFO Parsing config_dict 2019-01-16 11:54:10,229 snapperdb.fastq_to_vcf INFO Defining class variables and making output files 2019-01-16 11:54:10,233 snapperdb.fastq_to_vcf INFO Running Pheonix

timdallman commented 5 years ago

Hi. Looks like a GATK issue. What version are you using? v4 is not currently supported Tim

DolapoA commented 5 years ago

Seems to be resolved, Btw I'm using Gatk 3.7. But I'll get back to you to confirm.

DolapoA commented 5 years ago

All's well, you can close this. I needed to properly source/relaunch my .bash file.