./annovar.pl -t 10 -i demo_sample.avinput -r hg19 -o demo_sample
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile demo_sample.refGene -exonsort demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Output files were written to demo_sample.refGene.variant_function, demo_sample.refGene.exonic_variant_function
NOTICE: the queryfile contains 1479 lines
NOTICE: threading is disabled for gene-based annotation on file with less than 1000000 input lines
NOTICE: Reading gene annotation from /home/philippe/humandb/hg19_refGene.txt ... Done with 63481 transcripts (including 15216 without coding sequence annotation) for 27720 unique genes
NOTICE: Processing next batch with 1479 unique variants in 1479 input lines
NOTICE: Reading FASTA sequences from /home/philippe/humandb/hg19_refGeneMrna.fa ... Done with 319 sequences
WARNING: A total of 405 sequences will be ignored due to lack of correct ORF annotation
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=ensGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver hg19 -dbtype ensGene -outfile demo_sample.ensGene -exonsort demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Output files were written to demo_sample.ensGene.variant_function, demo_sample.ensGene.exonic_variant_function
NOTICE: the queryfile contains 1479 lines
NOTICE: threading is disabled for gene-based annotation on file with less than 1000000 input lines
NOTICE: Reading gene annotation from /home/philippe/humandb/hg19_ensGene.txt ... Done with 196501 transcripts (including 101155 without coding sequence annotation) for 57905 unique genes
NOTICE: Processing next batch with 1479 unique variants in 1479 input lines
NOTICE: Reading FASTA sequences from /home/philippe/humandb/hg19_ensGeneMrna.fa ... Done with 463 sequences
WARNING: A total of 6780 sequences will be ignored due to lack of correct ORF annotation
-----------------------------------------------------------------
NOTICE: Processing operation=r protocol=cytoBand
NOTICE: Running with system command <annotate_variation.pl -regionanno -dbtype cytoBand -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Output file is written to demo_sample.hg19_cytoBand
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_cytoBand.txt ... Done with 862 regions
NOTICE: Finished region-based annotation on 147 genetic variants
-----------------------------------------------------------------
NOTICE: Processing operation=r protocol=genomicSuperDups
NOTICE: Running with system command <annotate_variation.pl -regionanno -dbtype genomicSuperDups -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Output file is written to demo_sample.hg19_genomicSuperDups
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_genomicSuperDups.txt ... Done with 51599 regions
NOTICE: Finished region-based annotation on 147 genetic variants
-----------------------------------------------------------------
NOTICE: Processing operation=r protocol=gwasCatalog
NOTICE: Running with system command <annotate_variation.pl -regionanno -dbtype gwasCatalog -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Output file is written to demo_sample.hg19_gwasCatalog
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Finished region-based annotation on 147 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Reading annotation database /home/philippe/humandb/hg19_gwasCatalog.txt ... Done with 148736 regions
NOTICE: Finished region-based annotation on 148 genetic variants
NOTICE: Finished region-based annotation on 148 genetic variants
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=avsnp150
NOTICE: Running system command <annotate_variation.pl -filter -dbtype avsnp150 -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_avsnp150_dropped, other variants are written to demo_sample.hg19_avsnp150_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 140
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 142
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 138
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 128
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 130
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 133
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 140
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 140
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 133
NOTICE: Database index loaded. Total number of bins is 28258790 and the number of bins to be scanned is 135
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_avsnp150.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=esp6500siv2_all
NOTICE: Running system command <annotate_variation.pl -filter -dbtype esp6500siv2_all -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: the --dbtype esp6500siv2_all is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_esp6500siv2_all_dropped, other variants are written to demo_sample.hg19_esp6500siv2_all_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 47
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 57
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 60
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 57
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 42
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 64
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 51
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 55
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 53
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Database index loaded. Total number of bins is 594771 and the number of bins to be scanned is 68
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_esp6500siv2_all.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=1000g2015aug_all
NOTICE: Running system command <annotate_variation.pl -filter -dbtype 1000g2015aug_all -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_ALL.sites.2015_08_dropped, other variants are written to demo_sample.hg19_ALL.sites.2015_08_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 91
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 123
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 103
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 117
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 121
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 109
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 99
NOTICE: Database index loaded. Total number of bins is 2824642 and the number of bins to be scanned is 108
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_ALL.sites.2015_08.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=1000g2015aug_afr
NOTICE: Running system command <annotate_variation.pl -filter -dbtype 1000g2015aug_afr -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_AFR.sites.2015_08_dropped, other variants are written to demo_sample.hg19_AFR.sites.2015_08_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 121
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 91
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 109
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 117
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 123
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 103
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 99
NOTICE: Database index loaded. Total number of bins is 2820101 and the number of bins to be scanned is 108
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AFR.sites.2015_08.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=1000g2015aug_amr
NOTICE: Running system command <annotate_variation.pl -filter -dbtype 1000g2015aug_amr -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_AMR.sites.2015_08_dropped, other variants are written to demo_sample.hg19_AMR.sites.2015_08_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 108
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 109
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 123
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 91
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 124
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 117
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 102
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 121
NOTICE: Database index loaded. Total number of bins is 2815096 and the number of bins to be scanned is 99
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_AMR.sites.2015_08.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=1000g2015aug_eur
NOTICE: Running system command <annotate_variation.pl -filter -dbtype 1000g2015aug_eur -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_EUR.sites.2015_08_dropped, other variants are written to demo_sample.hg19_EUR.sites.2015_08_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 123
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 109
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 99
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 103
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 117
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 91
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 108
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 124
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2812033 and the number of bins to be scanned is 121
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EUR.sites.2015_08.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=1000g2015aug_eas
NOTICE: Running system command <annotate_variation.pl -filter -dbtype 1000g2015aug_eas -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_EAS.sites.2015_08_dropped, other variants are written to demo_sample.hg19_EAS.sites.2015_08_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 91
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 121
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 108
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 109
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 123
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 103
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 99
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2812769 and the number of bins to be scanned is 117
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_EAS.sites.2015_08.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=1000g2015aug_sas
NOTICE: Running system command <annotate_variation.pl -filter -dbtype 1000g2015aug_sas -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_SAS.sites.2015_08_dropped, other variants are written to demo_sample.hg19_SAS.sites.2015_08_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 117
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 108
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 91
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 103
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 109
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 124
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 99
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 123
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Database index loaded. Total number of bins is 2815886 and the number of bins to be scanned is 121
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_SAS.sites.2015_08.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=nci60
NOTICE: Running system command <annotate_variation.pl -filter -dbtype nci60 -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: the --dbtype nci60 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_nci60_dropped, other variants are written to demo_sample.hg19_nci60_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 41
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 53
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 36
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 37
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 48
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 43
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 40
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 43
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 34
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
NOTICE: Database index loaded. Total number of bins is 81308 and the number of bins to be scanned is 54
NOTICE: Scanning filter database /home/philippe/humandb/hg19_nci60.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=cosmic89_coding
NOTICE: Running system command <annotate_variation.pl -filter -dbtype cosmic89_coding -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: the --dbtype cosmic89_coding is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_cosmic89_coding_dropped, other variants are written to demo_sample.hg19_cosmic89_coding_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_coding.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=cosmic89_noncoding
NOTICE: Running system command <annotate_variation.pl -filter -dbtype cosmic89_noncoding -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10>
NOTICE: the --dbtype cosmic89_noncoding is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_cosmic89_noncoding_dropped, other variants are written to demo_sample.hg19_cosmic89_noncoding_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_cosmic89_noncoding.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=clinvar_20190305
NOTICE: Finished reading 5 column headers for '-dbtype clinvar_20190305'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype clinvar_20190305 -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10 -otherinfo>
NOTICE: the --dbtype clinvar_20190305 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_clinvar_20190305_dropped, other variants are written to demo_sample.hg19_clinvar_20190305_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 20
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 13
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 46
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 23
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 34
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 21
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 20
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 19
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 12
NOTICE: Database index loaded. Total number of bins is 45822 and the number of bins to be scanned is 51
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_clinvar_20190305.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=gnomad211_genome
NOTICE: Finished reading 17 column headers for '-dbtype gnomad211_genome'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype gnomad211_genome -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10 -otherinfo>
NOTICE: the --dbtype gnomad211_genome is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_gnomad211_genome_dropped, other variants are written to demo_sample.hg19_gnomad211_genome_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 140
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 128
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 138
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 140
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 142
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 135
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 130
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 133
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 140
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
NOTICE: Database index loaded. Total number of bins is 28119985 and the number of bins to be scanned is 133
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_genome.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=gnomad211_exome
NOTICE: Finished reading 17 column headers for '-dbtype gnomad211_exome'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype gnomad211_exome -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10 -otherinfo>
NOTICE: the --dbtype gnomad211_exome is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_gnomad211_exome_dropped, other variants are written to demo_sample.hg19_gnomad211_exome_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 69
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 47
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 78
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 69
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 58
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 66
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 67
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 74
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 54
NOTICE: Database index loaded. Total number of bins is 773145 and the number of bins to be scanned is 67
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_gnomad211_exome.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=exac03
NOTICE: Finished reading 8 column headers for '-dbtype exac03'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype exac03 -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10 -otherinfo>
NOTICE: the --dbtype exac03 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_exac03_dropped, other variants are written to demo_sample.hg19_exac03_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 67
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 72
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 66
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 67
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 68
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 76
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 55
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 47
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 53
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Database index loaded. Total number of bins is 749886 and the number of bins to be scanned is 64
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_exac03.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=intervar_20180118
NOTICE: Finished reading 29 column headers for '-dbtype intervar_20180118'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype intervar_20180118 -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10 -otherinfo>
NOTICE: the --dbtype intervar_20180118 is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_intervar_20180118_dropped, other variants are written to demo_sample.hg19_intervar_20180118_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 43
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 43
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 50
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 56
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 43
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 54
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 44
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 38
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 35
NOTICE: Database index loaded. Total number of bins is 530621 and the number of bins to be scanned is 37
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_intervar_20180118.txt...Done
-----------------------------------------------------------------
NOTICE: Processing operation=f protocol=dbnsfp31a_interpro
NOTICE: Finished reading 1 column headers for '-dbtype dbnsfp31a_interpro'
NOTICE: Running system command <annotate_variation.pl -filter -dbtype dbnsfp31a_interpro -buildver hg19 -outfile demo_sample demo_sample.avinput /home/philippe/humandb/ -thread 10 -otherinfo>
NOTICE: the --dbtype dbnsfp31a_interpro is assumed to be in generic ANNOVAR database format
NOTICE: Variants matching filtering criteria are written to demo_sample.hg19_dbnsfp31a_interpro_dropped, other variants are written to demo_sample.hg19_dbnsfp31a_interpro_filtered
NOTICE: the queryfile contains 1479 lines
NOTICE: Creating new threads for query line 1 to 148
NOTICE: Creating new threads for query line 149 to 296
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 297 to 444
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 445 to 592
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 593 to 740
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 741 to 888
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 889 to 1036
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1037 to 1184
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1185 to 1332
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Creating new threads for query line 1333 to 1479
NOTICE: Processing next batch with 148 unique variants in 148 input lines
NOTICE: Processing next batch with 147 unique variants in 147 input lines
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 21
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 23
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 21
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 26
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 30
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 22
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 22
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 18
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 11
NOTICE: Database index loaded. Total number of bins is 275326 and the number of bins to be scanned is 33
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
NOTICE: Scanning filter database /home/philippe/humandb/hg19_dbnsfp31a_interpro.txt...Done
-----------------------------------------------------------------
NOTICE: Multianno output file is written to demo_sample.hg19_multianno.txt
Finished
demo_sample log