Failed to call blastwise.pl

Question

[Yanpeng Chen]

Dear guys,

I am annotating a genome using the batch tool blastwise.pl in gene wise v2.4.1. I installed it successfully as the following test report, and I can call all sub-programs in bin the file. in wise2.4.1/src make test

 make test

cd test ; perl testman.pl -cf ../wisecfg < short.test
>>> Doing promoterwise promoterwise standard test
>>> Calling [../bin/promoterwise -silent pw.human pw.mouse > TEMP-PW]
>>> promoterwise ... Passed
>>> Doing basic-cdna cdna test case (protein v cdna), all outputs
>>> Calling [../bin/estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP]
>>> basic-cdna ... Passed
>>> Doing basic-genomic genomic test case (protein v genomic), all outputs
>>> Calling [../bin/genewise short.pep short.dna -pretty -para  -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear  > TEMP]
>>> basic-genomic ... Passed
>>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs
>>> Calling [../bin/estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer  short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP]
>>> hmm-binary-cdna ... Passed
>>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match
>>> Calling [../bin/genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP]
Information
        In making HSHNCPA1 a genomic sequence, converted 2 bases (0.5%) to
N's from non ATGCN
GeneWise6 Matrix calculation: [  32000] Cells 97%
>>> hmm-wrong-dna ... Passed
>>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match
>>> Calling [../bin/estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP]
Information
        In making HSHNCPA1 a cdna sequence, converted 2 bases (0.5%) to N's
from non ATGCN
EstWise3 Matrix calculation: [  32000] Cells 97%
EstWise3 Matrix calculation: [  32000] Cells 97%
>>> hmm-wrong-dna-est ... Passed
>>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs
>>> Calling [../bin/genewise -init local HMM.ascii -hmmer  short.dna -pretty -para  -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP]
>>> hmm-ascii-genomic ... Passed
>>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while
>>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP]
>>> genewise-db ... Passed
>>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while
>>> Calling [../bin/genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP]
>>> genewise-db-lite ... Passed
>>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while
>>> Calling [../bin/estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP]
>>> estwise-db ... Passed
>>> Doing pswdb Protein smith waterman db search
>>> Calling [../bin/pswdb road.pep pep.fa -quiet > TEMP ]
>>> pswdb ... Passed
>>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching
>>> Calling [../bin/genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP]
>>> genewisedb-pfam-mode ... Passed
Tests passed

But I can't call the ./blastwise.pl in wise2.4.1/src/perl/scripts, and the error report is showed as follow.

perl blastwise.pl

$perl blastwise.pl

The C-compiled engine for Wise2 has not been installed.  Please read
the installation instructions for Wise2 for building it

• bascially make perl at the top level

Next, I typed make perl in src directory, another exception occurred.

Could not find a typemap for C type 'Wise2_SupportingFeature *'. The following C types are mapped by the current typemap: 'AV *', 'Bits', 'Boolean', 'CV *', 'FILE *', 'FileHandle', 'HV *', 'I16', 'I32', 'I8', 'IV', 'InOutStream', 'InputStream', 'NV', 'OutputStream', 'PerlIO *', 'Probability', 'Result', 'STRLEN', 'SV *', 'SVREF', 'Score', 'SysRet', 'SysRetLong', 'Time_t *', 'U16', 'U32', 'U8', 'UV', 'Wise2_AlnBlock *', 'Wise2_AlnColumn *', 'Wise2_AlnRange *', 'Wise2_AlnRangeSet *', 'Wise2_AlnSequence *', 'Wise2_AlnUnit *', 'Wise2_CodonMapper *', 'Wise2_CodonTable *', 'Wise2_CompMat *', 'Wise2_ComplexSequence *', 'Wise2_ComplexSequenceEvalSet *', 'Wise2_DBSearchImpl *', 'Wise2_DataEntry *', 'Wise2_DataScore *', 'Wise2_DnaMatrix *', 'Wise2_DnaProbMatrix *', 'Wise2_DnaSequenceHitList *', 'Wise2_DnaStartEnd *', 'Wise2_Exon *', 'Wise2_FileSource *', 'Wise2_Gene *', 'Wise2_GeneConsensus *', 'Wise2_GeneFrequency21 *', 'Wise2_GeneParameter21 *', 'Wise2_GeneSingleCons *', 'Wise2_Genomic *', 'Wise2_GenomicDB *', 'Wise2_GenomicRegion *', 'Wise2_GenomicRepeat *', 'Wise2_Histogram *', 'Wise2_Hscore *', 'Wise2_MatchSummary *', 'Wise2_MatchSummarySet *', 'Wise2_PackAln *', 'Wise2_PackAlnUnit *', 'Wise2_PfamHmmer1DB *', 'Wise2_PfamHmmer1Entry *', 'Wise2_Protein *', 'Wise2_ProteinDB *', 'Wise2_RandomDNADB *', 'Wise2_RandomModel *', 'Wise2_RandomModelDNA *', 'Wise2_RandomProteinDB *', 'Wise2_SegmentHit *', 'Wise2_SegmentHitList *', 'Wise2_Sequence *', 'Wise2_SequenceDB *', 'Wise2_SequenceSet *', 'Wise2_ThreeStateDB *', 'Wise2_ThreeStateModel *', 'Wise2_ThreeStateUnit *', 'Wise2_Transcript *', 'Wise2_Translation *', 'Wise2_cDNA *', 'Wise2_cDNADB *', 'Wise2_cDNAParser *', 'aa', 'base', 'bool', 'bool_t', 'boolean', 'caddr_t', 'char', 'char *', 'char **', 'codon', 'const char *', 'double', 'float', 'int', 'long', 'short', 'size_t', 'ssize_t', 'time_t', 'unsigned', 'unsigned char', 'unsigned char *', 'unsigned int', 'unsigned long', 'unsigned long *', 'unsigned short', 'void', 'void *', 'wchar_t', 'wchar_t *'  in Wise2.xs, line 6189 
Could not find a typemap for C type 'Wise2_SupportingFeature *'. 
The following C types are mapped by the current typemap: 'AV *', 'Bits', 'Boolean', 'CV *', 'FILE *', 'FileHandle', 'HV *', 'I16', 'I32', 'I8', 'IV', 'InOutStream', 'InputStream', 'NV', 'OutputStream', 'PerlIO *', 'Probability', 'Result', 'STRLEN', 'SV *', 'SVREF', 'Score', 'SysRet', 'SysRetLong', 'Time_t *', 'U16', 'U32', 'U8', 'UV', 'Wise2_AlnBlock *', 'Wise2_AlnColumn *', 'Wise2_AlnRange *', 'Wise2_AlnRangeSet *', 'Wise2_AlnSequence *', 'Wise2_AlnUnit *', 'Wise2_CodonMapper *', 'Wise2_CodonTable *', 'Wise2_CompMat *', 'Wise2_ComplexSequence *', 'Wise2_ComplexSequenceEvalSet *', 'Wise2_DBSearchImpl *', 'Wise2_DataEntry *', 'Wise2_DataScore *', 'Wise2_DnaMatrix *', 'Wise2_DnaProbMatrix *', 'Wise2_DnaSequenceHitList *', 'Wise2_DnaStartEnd *', 'Wise2_Exon *', 'Wise2_FileSource *', 'Wise2_Gene *', 'Wise2_GeneConsensus *', 'Wise2_GeneFrequency21 *', 'Wise2_GeneParameter21 *', 'Wise2_GeneSingleCons *', 'Wise2_Genomic *', 'Wise2_GenomicDB *', 'Wise2_GenomicRegion *', 'Wise2_GenomicRepeat *', 'Wise2_Histogram *', 'Wise2_Hscore *', 'Wise2_MatchSummary *', 'Wise2_MatchSummarySet *', 'Wise2_PackAln *', 'Wise2_PackAlnUnit *', 'Wise2_PfamHmmer1DB *', 'Wise2_PfamHmmer1Entry *', 'Wise2_Protein *', 'Wise2_ProteinDB *', 'Wise2_RandomDNADB *', 'Wise2_RandomModel *', 'Wise2_RandomModelDNA *', 'Wise2_RandomProteinDB *', 'Wise2_SegmentHit *', 'Wise2_SegmentHitList *', 'Wise2_Sequence *', 'Wise2_SequenceDB *', 'Wise2_SequenceSet *', 'Wise2_ThreeStateDB *', 'Wise2_ThreeStateModel *', 'Wise2_ThreeStateUnit *', 'Wise2_Transcript *', 'Wise2_Translation *', 'Wise2_cDNA *', 'Wise2_cDNADB *', 'Wise2_cDNAParser *', 'aa', 'base', 'bool', 'bool_t', 'boolean', 'caddr_t', 'char', 'char *', 'char **', 'codon', 'const char *', 'double', 'float', 'int', 'long', 'short', 'size_t', 'ssize_t', 'time_t', 'unsigned', 'unsigned char', 'unsigned char *', 'unsigned int', 'unsigned long', 'unsigned long *', 'unsigned short', 'void', 'void *', 'wchar_t', 'wchar_t *'  in Wise2.xs, line 6216 
make[1]: ***
[Wise2.c] Error 1

Anyone else has got these exception? How did you solve it? Is this a error resulted from Perl version?

Thanks!