SNPSVM - not able to find VCF file

Question

[Ramana]

I generated a sorted bamfile what to call variants. I provided a list of files. hg38.fa, hg38.fa.fi (indexfile) ,SRR098401_PE_bwtsort.bam,SRR098401mem_pesortbam (indexfile), Aligner - Bowtie2 Variant - SNPSVM I want to known whether it is running correctly ? Prompt Seems to be like this. I'm not able to find VCF file ? Command: java -jar snpsvm.jar predict -R /data/guest/Softwares/novocraft/hg38.fa -B /data/guest/SRR098401_PE_bwtsort.bam -M /data/guest/Softwares/SNPSVM-master/models/default.model -V SRR098401SNPSVM.raw.vcf Loading module class snpsvm.app.Predictor Calling SNPs over 3209286105 bases with 4 threads in 473 chunks Elapsed Bases Bases / sec % Complete mem - 0:05.87 312188 53192.71 0.01% 234MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.ELXTXjsh0QT7.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.ELXTXjsh0QT7.data.461.output reported an error java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.ELXTXjsh0QT7.data.461.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641) at java.base/java.lang.Thread.run(Thread.java:844) \ 1:36.94 489033 5044.54 0.02% 32MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.ZdgswnLs1dSr.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.ZdgswnLs1dSr.data.904.output reported an error java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.ZdgswnLs1dSr.data.904.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641) at java.base/java.lang.Thread.run(Thread.java:844) | 1:50.78 9138704 82494.91 0.28% 444MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.04J3WyaQOtPC.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.04J3WyaQOtPC.data.550.output reported an error java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.04J3WyaQOtPC.data.550.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641) at java.base/java.lang.Thread.run(Thread.java:844) \ 1:55.39 17788375 154157.39 0.55% 221MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.6xtu3ABy3xsn.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.6xtu3ABy3xsn.data.315.output reported an error java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.6xtu3ABy3xsn.data.315.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641) at java.base/java.lang.Thread.run(Thread.java:844) / 2:02.94 26438045 215051.86 0.82% 96MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.rWXGLJbYYzsK.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.rWXGLJbYYzsK.data.860.output reported an error java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.rWXGLJbYYzsK.data.860.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641) at java.base/java.lang.Thread.run(Thread.java:844) \ 2:10.49 35087716 268902.30 1.09% 65MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.ukBbMFk1N9bH.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.ukBbMFk1N9bH.data.575.output reported an error java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.ukBbMFk1N9bH.data.575.output does not exist at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39) at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641) at java.base/java.lang.Thread.run(Thread.java:844)

Answer 1

[pfs]

Is the vcf file located in the directory you are trying to execute the program? If not go back and include the path after the -V argument.

[Ramana]

Hi, again same error Command: [guest@ibscmachine SNPSVM-master]$ java -jar snpsvm.jar predict -R /data/guest/Softwares/novocraft/hg38.fa -B /data/guest/SNPSVM/SRR098401mem_pesort.bam -M /data/guest/Softwares/SNPSVM-master/models/default.model -V /data/guest/SNPSVM/SRR098401SNPSVM_mem1.raw.vcf Loading module class snpsvm.app.Predictor Calling SNPs over 3209286105 bases with 4 threads in 473 chunks
Elapsed Bases Bases / sec % Complete mem
- 0:02.52 312188 123982.53 0.01% 128MBWarning: libsvm process executing command /data/guest/Softwares/libsvm-mastersvm-predict -b 1 /data/guest/Softwares/SNPSVM-master/.x2FxBQPUwjyk.data /data/guest/Softwares/SNPSVM-master/models/default.model /data/guest/Softwares/SNPSVM-master/.x2FxBQPUwjyk.data.421.output reported an error
java.lang.IllegalStateException: Result file /data/guest/Softwares/SNPSVM-master/.x2FxBQPUwjyk.data.421.output does not exist
at snpsvm.bamreading.ResultVariantConverter.createVariantList(ResultVariantConverter.java:39)
at snpsvm.bamreading.SNPCaller.run(SNPCaller.java:92)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641)

Answer 2

[pfs]

Have you told SNPSVM where libsvm is? See installation step 3. https://github.com/brendanofallon/SNPSVM

[Ramana]

HI

Sorry, for late response, I given the path still it is not generating the output file.