SNPSVM - not able to find VCF file
2
0
Entering edit mode
6.4 years ago
Ramana • 0

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)

sequence • 1.3k views
ADD COMMENT
0
Entering edit mode
6.4 years ago
pfs ▴ 280

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.

ADD COMMENT
0
Entering edit mode

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)

ADD REPLY
0
Entering edit mode
6.4 years ago
pfs ▴ 280

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

ADD COMMENT
0
Entering edit mode

HI

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

ADD REPLY

Login before adding your answer.

Traffic: 2675 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6