SNPSVM
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SNPSVM not generating output
Its showing error.
Commandjava -Xmx8g -jar snpsvm.jar predict -R /home/likithreddy/Documents/Genome/hg38.fa -B /media/likithreddy/D1_SEQ_DATA/LikithReddy/SRR098401mem_pesort.bam -M /home/likithreddy/Downloads/SNPSVM-master/models/default.model -V out.vcf
Loading module class snpsvm.app.Predictor Calling SNPs over 3209286105 bases with 4 threads in 473 chunks Elapsed Bases Bases / sec % Complete mem
- 0:04.19 312188 74507.88 0.01% 525MBWarning: libsvm process executing command /home/likithreddy/Downloads/SNPSVM-master/libsvm-mastersvm-predict -b 1 /home/likithreddy/Downloads/SNPSVM-master/.fe5KC1OEaJ1q.data /home/likithreddy/Downloads/SNPSVM-master/models/default.model /home/likithreddy/Downloads/SNPSVM-master/.fe5KC1OEaJ1q.data.829.output reported an error java.lang.IllegalStateException: Result file /home/likithreddy/Downloads/SNPSVM-master/.fe5KC1OEaJ1q.data.829.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) \ | 1:07.08 489033 7289.75 0.02%