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zzhang526 / MosaicHunter

A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples.
http://mosaichunter.cbi.pku.edu.cn/
MIT License
12 stars 4 forks source link

FilterFactory error: "filter name is null" #8

Closed amyyxt closed 2 years ago

amyyxt commented 2 years ago

Hello!

I'm trying to run MH for WES but have come across this error:

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.simontuffs.onejar.Boot.run(Boot.java:342)
    at com.simontuffs.onejar.Boot.main(Boot.java:168)
Caused by: java.lang.IllegalArgumentException: filter name is null.
    at cn.edu.pku.cbi.mosaichunter.filter.FilterFactory.create(FilterFactory.java:33)
    at cn.edu.pku.cbi.mosaichunter.BamScanner.<init>(BamScanner.java:78)
    at cn.edu.pku.cbi.mosaichunter.MosaicHunter.main(MosaicHunter.java:96)
    ... 6 more

An example command I used to call MH that led to this error is:

java -jar */MosaicHunter/build/mosaichunter.jar -C */MosaicHunter/conf/exome_parameter.properties -P reference_file=*/MosaicHunter/resources/human_g1k_v37.fasta -P repetitive_region_filter.bed_file=*/MosaicHunter/resources/all_repeats.b37.bed -P common_site_filter.bed_file=*/MosaicHunter/resources/WES_Agilent_71M.error_prone.b37.bed -P mosaic_filter.dbsnp_file=*/MosaicHunter/resources/dbsnp_137.b37.tsv -P input_file=*/MosaicHunter_runs/subcut_nodules_mchris/data/PiEx@@MChris-0001-01@@A494_rea_recal.bam -P mosaic_filter.sex=F -P mosaic_filter.mode=paired_naive -P mosaic_filter.control_bam_file=*/MosaicHunter_runs/subcut_nodules_mchris/data/PiEx@@MChris-0001-04@@A503_rea_recal.bam -P output_dir=*/MosaicHunter_runs/subcut_nodules_mchris/out_1_estimate/MChris-0001_paired_naive

The exome_parameter.properties is nearly identical to the corresponding sample you provide in this repo, with the only changes being to reference/error-filtering filepaths (reference_file, repeptitive_region_filter.bed_file, common_site_filter.bec_file, and mosaic_filter.dbsnp_file), which are the same as specified in the example command provided above, and the name for output_dir.

I tried to track down the chunk of code (e.g. in FilterFactory.java, BamScanner.java, etc.) related to the error in hopes of figuring out what I may be doing wrong but do not understand what is happening. Would you help me troubleshoot, please? Thank you!

Best, Amy

amyyxt commented 2 years ago

Looks like this was due to a typo on my part! Sorry about the confusion!