#60 Errors while installing vcftools
Hello,
I encountered the following errors while installing vcftools. I have my tabix folder inside vcf tools folder. I also changed the path to the path of tabix. I am unable to figure out how to verify bgzip installation. please help me in this regards
Thanks
Prathyusha
sh: 1: bgzip: not found
not ok 1 - Is bgzip OK? .. cat /media/wkstn/Data/vcftools_0.1.13/perl/../examples/merge-test-a.vcf | bgzip -c > /media/wkstn/Data/vcftools_0.1.13/perl/../examples/merge-test-a.vcf.gz
Failed test 'Is bgzip OK? .. cat /media/wkstn/Data/vcftools_0.1.13/perl/../examples/merge-test-a.vcf | bgzip -c > /media/wkstn/Data/vcftools_0.1.13/perl/../examples/merge-test-a.vcf.gz'
at test.t line 66.
got: '32512'
expected: '0'
Can't exec "tabix": No such file or directory at test.t line 69.
not ok 2 - Is tabix OK? .. tabix /media/wkstn/Data/vcftools_0.1.13/perl/../examples/merge-test-a.vcf.gz
Failed test 'Is tabix OK? .. tabix /media/wkstn/Data/vcftools_0.1.13/perl/../examples/merge-test-a.vcf.gz'
at test.t line 70.
got: '-1'
expected: '0'
not ok 14 - Testing vcf-stats .. perl -I/media/wkstn/Data/vcftools_0.1.13/perl -MVcf /media/wkstn/Data/vcftools_0.1.13/perl/vcf-stats /media/wkstn/Data/vcftools_0.1.13/perl/../examples/valid-4.0.vcf
Failed test 'Testing vcf-stats .. perl -I/media/wkstn/Data/vcftools_0.1.13/perl -MVcf /media/wkstn/Data/vcftools_0.1.13/perl/vcf-stats /media/wkstn/Data/vcftools_0.1.13/perl/../examples/valid-4.0.vcf'
at test.t line 165.
Structures begin differing at:
$got->[4] = ' 'het_AA_count' => 1,
'
$expected->[4] = ' 'indel' => {
'
ok 15 - Testing add_columns with genotypes full, 4.0.
ok 16 - Testing add_columns with genotypes brief, 4.0.
ok 17 - Testing add_columns brief, 4.0.
ok 18 - Testing add_columns no gtypes, 4.0.
sh: 1: bgzip: not found
sh: 1: tabix: not found
sh: 1: bgzip: not found
sh: 1: tabix: not found
sh: 1: bgzip: not found
sh: 1: tabix: not found
not ok 19 - Testing vcf-merge .. perl -I../perl/ -MVcf ../perl/vcf-merge merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz
Failed test 'Testing vcf-merge .. perl -I../perl/ -MVcf ../perl/vcf-merge merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz'
at test.t line 252.
Structures begin differing at:
$got->[0] = Does not exist
$expected->[0] = '##fileformat=VCFv4.2
'
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 218.
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 218.
gzip: cmp-test-a.vcf.gz: unexpected end of file
Broken VCF header, no column names?
at ../perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x2257840), "Broken VCF header, no column names?") called at ../perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x2257840)) called at ../perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x2257840)) called at ../perl/vcf-compare line 198
main::compare_vcfs(HASH(0x21ab360)) called at ../perl/vcf-compare line 19
not ok 20 - Testing vcf-compare .. perl -I../perl/ -MVcf ../perl/vcf-compare -g cmp-test-a.vcf.gz cmp-test-b.vcf.gz | grep -v '^# The command'
Failed test 'Testing vcf-compare .. perl -I../perl/ -MVcf ../perl/vcf-compare -g cmp-test-a.vcf.gz cmp-test-b.vcf.gz | grep -v '^# The command''
at test.t line 229.
Structures begin differing at:
$got->[2] = Does not exist
$expected->[2] = '#VN 'Venn-Diagram Numbers'. Use grep ^VN | cut -f 2- to extract this part.
'
sh: 1: bgzip: not found
sh: 1: tabix: not found
sh: 1: bgzip: not found
sh: 1: tabix: not found
sh: 1: bgzip: not found
sh: 1: tabix: not found
not ok 21 - Testing vcf-isec .. perl -I../perl/ -MVcf ../perl/vcf-isec -f -n +2 merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz
Failed test 'Testing vcf-isec .. perl -I../perl/ -MVcf ../perl/vcf-isec -f -n +2 merge-test-a.vcf.gz merge-test-b.vcf.gz merge-test-c.vcf.gz'
at test.t line 275.
Structures begin differing at:
$got->[0] = '
'
$expected->[0] = 'Warning: The column names do not match (e.g. B):
ok 23 - Testing vcf-shuffle-cols .. perl -I../perl/ -MVcf ../perl/vcf-shuffle-cols -t cmp-test-a.vcf shuffle-test.vcf
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 328.
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 328.
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 328.
not ok 24 - Testing vcf-concat .. perl -I../perl/ -MVcf ../perl/vcf-concat -s 3 concat-a.vcf.gz concat-b.vcf.gz concat-c.vcf.gz
Failed test 'Testing vcf-concat .. perl -I../perl/ -MVcf ../perl/vcf-concat -s 3 concat-a.vcf.gz concat-b.vcf.gz concat-c.vcf.gz'
at test.t line 338.
Structures begin differing at:
$got->[0] = '
'
$expected->[0] = '##fileformat=VCFv4.0
'
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 355.
not ok 25 - Testing vcf-annotate .. perl -I../perl/ -MVcf ../perl/vcf-annotate -c FROM,TO,CHROM,-,-,-,INFO/HM2,INFO/GN,INFO/DP -d key=INFO,ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership" -d key=INFO,ID=GN,Number=1,Type=String,Description="Gene Name" -d key=INFO,ID=DP,Number=0,Type=Integer,Description="Depth,etc" concat-a.vcf -a annotate.txt.gz
Failed test 'Testing vcf-annotate .. perl -I../perl/ -MVcf ../perl/vcf-annotate -c FROM,TO,CHROM,-,-,-,INFO/HM2,INFO/GN,INFO/DP -d key=INFO,ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership" -d key=INFO,ID=GN,Number=1,Type=String,Description="Gene Name" -d key=INFO,ID=DP,Number=0,Type=Integer,Description="Depth,etc" concat-a.vcf -a annotate.txt.gz'
at test.t line 365.
Structures begin differing at:
$got->[9] = 'Can't exec "tabix": No such file or directory at ../perl/vcf-annotate line 1391, <ANONIO> line 8.
'
$expected->[9] = '1 100 . GTTT G 1806 q10 DP=5;GN=gene1;HM2 GT:GQ:DP 0/1:409:35
'
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 355.
not ok 26 - Testing vcf-annotate .. perl -I../perl/ -MVcf ../perl/vcf-annotate -c FROM,TO,CHROM,ID,REF,ALT,INFO/HM2,INFO/GN,INFO/DP -d key=INFO,ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership" -d key=INFO,ID=GN,Number=1,Type=String,Description="Gene Name" -d key=INFO,ID=DP,Number=0,Type=Integer,Description="Depth,etc" concat-a.vcf -a annotate.txt.gz
Failed test 'Testing vcf-annotate .. perl -I../perl/ -MVcf ../perl/vcf-annotate -c FROM,TO,CHROM,ID,REF,ALT,INFO/HM2,INFO/GN,INFO/DP -d key=INFO,ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership" -d key=INFO,ID=GN,Number=1,Type=String,Description="Gene Name" -d key=INFO,ID=DP,Number=0,Type=Integer,Description="Depth,etc" concat-a.vcf -a annotate.txt.gz'
at test.t line 365.
Structures begin differing at:
$got->[9] = 'Can't exec "tabix": No such file or directory at ../perl/vcf-annotate line 1391, <ANONIO> line 8.
'
$expected->[9] = '1 100 id1_100 GTTT G 1806 q10 DP=5;GN=gene1;HM2 GT:GQ:DP 0/1:409:35
'
not ok 27 - Testing vcf-annotate .. perl -I../perl/ -MVcf ../perl/vcf-annotate -f +/D=34/c=2,3 annotate-test.vcf
Failed test 'Testing vcf-annotate .. perl -I../perl/ -MVcf ../perl/vcf-annotate -f +/D=34/c=2,3 annotate-test.vcf'
at test.t line 365.
Structures begin differing at:
$got->[8] = '##FILTER=<id=minmq,description="minimum rms="" mapping="" quality="" for="" snps="" (info="" mq)="" <span="">[10]"></id=minmq,description="minimum>
'
$expected->[8] = '##FILTER=<id=enddistbias,description="min p-value="" for="" end="" distance="" bias="" (info="" pv4)="" <span="">[0.0001]"></id=enddistbias,description="min>
'
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 412.
gzip: consensus.vcf.gz: unexpected end of file
Broken VCF header, no column names?
at ../perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x1ceca00), "Broken VCF header, no column names?") called at ../perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x1ceca00)) called at ../perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x1ceca00)) called at ../perl/vcf-consensus line 80
main::do_consensus(HASH(0x1cc0f30)) called at ../perl/vcf-consensus line 9
not ok 30 - Testing vcf-consensus .. perl -I../perl/ -MVcf ../perl/vcf-consensus consensus.vcf.gz < consensus.fa
Failed test 'Testing vcf-consensus .. perl -I../perl/ -MVcf ../perl/vcf-consensus consensus.vcf.gz < consensus.fa'
at test.t line 420.
Structures begin differing at:
$got->[0] = Does not exist
$expected->[0] = '>1:1-500
'
sh: 1: bgzip: not found
Can't exec "tabix": No such file or directory at test.t line 412.
gzip: consensus.vcf.gz: unexpected end of file
Broken VCF header, no column names?
at ../perl/Vcf.pm line 172.
Vcf::throw(Vcf4_2=HASH(0x272fa58), "Broken VCF header, no column names?") called at ../perl/Vcf.pm line 866
VcfReader::_read_column_names(Vcf4_2=HASH(0x272fa58)) called at ../perl/Vcf.pm line 601
VcfReader::parse_header(Vcf4_2=HASH(0x272fa58)) called at ../perl/vcf-consensus line 80
main::do_consensus(HASH(0x2703f30)) called at ../perl/vcf-consensus line 9
not ok 31 - Testing vcf-consensus .. perl -I../perl/ -MVcf ../perl/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa
Failed test 'Testing vcf-consensus .. perl -I../perl/ -MVcf ../perl/vcf-consensus -s NA001 consensus.vcf.gz < consensus.fa'
at test.t line 420.
Structures begin differing at:
$got->[0] = Does not exist
$expected->[0] = '>1:1-500
'
not ok 32 - Testing vcf-contrast .. perl -I../perl/ -MVcf ../perl/vcf-contrast -n +D -A,B,C -d 10 contrast.vcf | grep -v ^##source
Failed test 'Testing vcf-contrast .. perl -I../perl/ -MVcf ../perl/vcf-contrast -n +D -A,B,C -d 10 contrast.vcf | grep -v ^##source'
at test.t line 436.
Structures begin differing at:
$got->[48] = '1 17538 . C A 64 MinMQ DP=393;VDB=0.0314;AF1=0.125;AC1=1;DP4=138,205,17,27;MQ=28;FQ=64;PV4=0.87,0.32,1,1;AN=8;AC=1;NOVELTY=29;NOVELAL=D GT:PL:DP:SP:GQ 0/0:0,152,255:148:1:99 0/0:0,29,227:72:4:34 0/0:0,71,255:86:6:76 0/1:70,0,226:81:4:65
'
$expected->[48] = '1 17538 . C A 64 MinMQ DP=393;VDB=0.0314;AF1=0.125;AC1=1;DP4=138,205,17,27;MQ=28;FQ=64;PV4=0.87,0.32,1,1;AN=8;AC=1;NOVELAL=D;NOVELTY=29 GT:PL:DP:SP:GQ 0/0:0,152,255:148:1:99 0/0:0,29,227:72:4:34 0/0:0,71,255:86:6:76 0/1:70,0,226:81:4:65
'
not ok 33 - Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../perl/ -MVcf ../perl/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n'
Failed test 'Testing vcf-fix-ploidy .. cat fix-ploidy.vcf | perl -I../perl/ -MVcf ../perl/vcf-fix-ploidy -s fix-ploidy.samples -p fix-ploidy.txt 2>/dev/null | vcf-query -f '%POS[\t%SAMPLE %GTR %PL]\n''
at test.t line 452.
Structures begin differing at:
$got->[0] = 'sh: 1: vcf-query: not found
'
$expected->[0] = '61098 M1 0 0,9,72,5,6,7 M2 0 0,15,140,5,6,7 F3 1/1 147,0,5 F4 0/0 0,131,5 M5 0 0,9,83,5,6,7 M6 0 0,6,56,5,6,7
'
Looks like you failed 14 tests of 75.
