>creating p-loci data structure...done
 -> selfscore (ENSP00000364438) successfully validated...
WARNING: Best-reference-hit is not on the same chromosome/contig as the reference!
 -> the selfscore for query protein "ENSP00000364396" is NOT valid!
WARNING: Best-reference-hit is not on the same chromosome/contig as the reference!
 -> the selfscore for query protein "ENSP00000364321" is NOT valid!
 -> selfscore (ENSP00000364349) successfully validated...
 -> selfscore (ENSP00000364298) successfully validated...
 -> selfscore (ENSP00000364291) successfully validated...
 -> selfscore (ENSP00000364285) successfully validated...
 -> selfscore (ENSP00000337463) successfully validated...
 -> selfscore (ENSP00000364235) successfully validated...
WARNING: Best-reference-hit is not on the same chromosome/contig as the reference!
 -> the selfscore for query protein "ENSP00000364211" is NOT valid!
 -> selfscore (ENSP00000364190) successfully validated...
 -> selfscore (ENSP00000364180) successfully validated...
WARNING: Best-reference-hit is not on the same chromosome/contig as the reference!
 -> the selfscore for query protein "ENSP00000364163" is NOT valid!
WARNING: Best-reference-hit is not on the same chromosome/contig as the reference!
 -> the selfscore for query protein "ENSP00000364156" is NOT valid!
 -> selfscore (ENSP00000364141) successfully validated...
>fetching global-besthit data for all queries against Gallus_gallus...>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364438"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364298"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364291"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364285"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364211"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364180"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364156"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gallus_gallus.blastresult contains no data (at least for query "ENSP00000364141"! (getBestBlastHit)
done
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204338, targetOrg=Gallus_gallus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168477, targetOrg=Gallus_gallus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204319, targetOrg=Gallus_gallus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204315, targetOrg=Gallus_gallus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204314, targetOrg=Gallus_gallus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168452, targetOrg=Gallus_gallus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204310, targetOrg=Gallus_gallus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204308, targetOrg=Gallus_gallus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204305, targetOrg=Gallus_gallus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204304, targetOrg=Gallus_gallus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204301, targetOrg=Gallus_gallus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204297, targetOrg=Gallus_gallus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204296, targetOrg=Gallus_gallus)...none
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>fetching global-besthit data for all queries against Canis_familiaris...>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Canis_familiaris.blastresult contains no data (at least for query "ENSP00000364156"! (getBestBlastHit)
done
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204338, targetOrg=Canis_familiaris)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168477, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204319, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204315, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204314, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168452, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204310, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204308, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204305, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204304, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204301, targetOrg=Canis_familiaris)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204297, targetOrg=Canis_familiaris)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204296, targetOrg=Canis_familiaris)...none
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>fetching global-besthit data for all queries against Macaca_mulatta...done
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204338, targetOrg=Macaca_mulatta)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168477, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204319, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204315, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204314, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168452, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204310, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204308, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204305, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204304, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204301, targetOrg=Macaca_mulatta)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204297, targetOrg=Macaca_mulatta)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204296, targetOrg=Macaca_mulatta)...ok
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>fetching global-besthit data for all queries against Gasterosteus_aculeatus...>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gasterosteus_aculeatus.blastresult contains no data (at least for query "ENSP00000364438"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gasterosteus_aculeatus.blastresult contains no data (at least for query "ENSP00000364291"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gasterosteus_aculeatus.blastresult contains no data (at least for query "ENSP00000364180"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gasterosteus_aculeatus.blastresult contains no data (at least for query "ENSP00000364156"! (getBestBlastHit)
>warning: tblastn/PBX2_ENSG00000204304_2e5.protein.info.Gasterosteus_aculeatus.blastresult contains no data (at least for query "ENSP00000364141"! (getBestBlastHit)
done
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204338, targetOrg=Gasterosteus_aculeatus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168477, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204319, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204315, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204314, targetOrg=Gasterosteus_aculeatus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168452, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204310, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204308, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204305, targetOrg=Gasterosteus_aculeatus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204304, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204301, targetOrg=Gasterosteus_aculeatus)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204297, targetOrg=Gasterosteus_aculeatus)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204296, targetOrg=Gasterosteus_aculeatus)...none
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_2051" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_8720" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_1090" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_10000" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_4301" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_1256" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_8547" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_4828" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_1846" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...Argument "contig_9233" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
>fetching global-besthit data for all queries against Homo_sapiens...done
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204338, targetOrg=Homo_sapiens)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168477, targetOrg=Homo_sapiens)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204319, targetOrg=Homo_sapiens)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204315, targetOrg=Homo_sapiens)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204314, targetOrg=Homo_sapiens)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000168452, targetOrg=Homo_sapiens)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204310, targetOrg=Homo_sapiens)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204308, targetOrg=Homo_sapiens)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204305, targetOrg=Homo_sapiens)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204304, targetOrg=Homo_sapiens)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204301, targetOrg=Homo_sapiens)...ok
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204297, targetOrg=Homo_sapiens)...none
>fetching EnsemblCompara-homologs for (GeneID=ENSG00000204296, targetOrg=Homo_sapiens)...none
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...Argument "c6_COX" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...Argument "c6_QBL" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 465.
done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "NoData" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/lib/perl5/5.8.8/SynBlast/MySyntenyAln.pm line 893.
>chaining blast-hits together...done
>calculating gene order alignments...done
Argument "contig_1256" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/bin/doSyntenyAlignment.pl line 1032.
>"ENSG00000204304-homologs/comparaHits/Homo_sapiens.ENSP00000364190.fa" did already exist, skip downloading...
>"ENSG00000204304-homologs/comparaHits/Homo_sapiens.ENSP00000364190.fa" did already exist, skip downloading...
>"ENSG00000204304-homologs/comparaHits/Homo_sapiens.ENSP00000364190.fa" did already exist, skip downloading...
Argument "c6_COX" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/bin/doSyntenyAlignment.pl line 1032.
Argument "c6_QBL" isn't numeric in int at /homes/bierdepot/joe/MyLocalSrcDir/perl/bin/doSyntenyAlignment.pl line 1032.