Error with libsvm and utils.py

[jessicakan789]

I installed libsvm 3.32 and got this error with PredPSI-SVM

./main.sh example/sample.vcf -o example/outdir 

>>== Check commands availablity ==<< 

/usr/bin/python 

/usr/bin/python3 

/usr/bin/perl 

/usr/bin/samtools 

** ERROR: check variable "svm_scale" in src/init.sh 

** ERROR: check variable "svm_predict" in src/init.sh 

** ANNOVAR annotating...... 

NOTICE: Finished reading 99 lines from VCF file 

NOTICE: A total of 99 locus in VCF file passed QC threshold, representing 99 SNPs (77 transitions and 22 transversions) and 0 indels/substitutions 

NOTICE: Finished writting 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions for 1 sample 

NOTICE: The --geneanno operation is set to ON by default 

NOTICE: Reading gene annotation from /data/jess_tmp/fh/PredPSI-SVR/tools/annovar/humandb/hg19_ensGene.txt ... Done with 103433 transcripts (including 38799 without coding sequence annotation) for 47132 unique genes 

NOTICE: Finished gene-based annotation on 0 genetic variants in /data/jess_tmp/fh/PredPSI-SVR/example/outdir/input.avinput 

NOTICE: Output files were written to /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.variant_function, /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.exonic_variant_function 

    DONE 

** Preparing mutation info... 

  - only vcf, finding exon transcript... 

/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:30: SyntaxWarning: "is" with a literal. Did you mean "=="? 

  assert errmsg is '', "Error in file 'utils.py':'get_genome': " + errmsg 

/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:51: SyntaxWarning: "is" with a literal. Did you mean "=="? 

  if len(args) is 0: 

/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:118: SyntaxWarning: "is" with a literal. Did you mean "=="? 

  if self.strand is '-': 

/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:292: SyntaxWarning: "is" with a literal. Did you mean "=="? 

  if strand is '+': 

However, you can fix it by doing

chmod -x svm-predict.c 

chmod -x svm-scale.c 

And change all the "is" in util.py to "=="

This gives

./main.sh example/sample.vcf -o example/outdir 

>>== Check commands availablity ==<< 

/usr/bin/python 

/usr/bin/python3 

/usr/bin/perl 

/usr/bin/samtools 

/data/jess_tmp/fh/PredPSI-SVR/tools/libsvm-3.32/svm-scale.c 

/data/jess_tmp/fh/PredPSI-SVR/tools/libsvm-3.32/svm-predict.c 

** ANNOVAR annotating...... 

NOTICE: Finished reading 99 lines from VCF file 

NOTICE: A total of 99 locus in VCF file passed QC threshold, representing 99 SNPs (77 transitions and 22 transversions) and 0 indels/substitutions 

NOTICE: Finished writting 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions for 1 sample 

NOTICE: The --geneanno operation is set to ON by default 

NOTICE: Reading gene annotation from /data/jess_tmp/fh/PredPSI-SVR/tools/annovar/humandb/hg19_ensGene.txt ... Done with 103433 transcripts (including 38799 without coding sequence annotation) for 47132 unique genes 

NOTICE: Finished gene-based annotation on 0 genetic variants in /data/jess_tmp/fh/PredPSI-SVR/example/outdir/input.avinput 

NOTICE: Output files were written to /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.variant_function, /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.exonic_variant_function 

    DONE 

** Preparing mutation info... 

  - only vcf, finding exon transcript... 

I haven't got OUTPUT.dpsi but that might be because I haven't got the SPIDEX database installed yet (still waiting for a link)

/PredPSI-SVR/example/outdir$ ls

annovar.exonic_variant_function  annovar.log  annovar.variant_function  input.avinput  input.vcf  mut_info  mut_info.valid

[chenkenbio]

Hello, sorry for my late reply. Have you downloaded the SPIDEX database yet? http://www.openbioinformatics.org/annovar/spidex_download_form.php

[jessicakan789]

I tried twice over a period of 2 weeks but haven't received anything yet