Dear future person who gets the same error I had,<br><br>I thought people might like to know after asking on the 1000genome address that the problem was down to attempting to analyse too large a segment of genome at once, which apparently causes a bug in Tabix which results in the variable error message about expected data.<br>
<br>Using a smaller set of data at a time solves the problem.<br><br>Thanks,<br><br>Nick<br><br><div class="gmail_quote">On 20 February 2013 11:24, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Nick,<div><br></div><div>I believe this tool has been developed by the 1000 Genomes project people - I'd suggest contacting them at <a href="mailto:info@1000genomes.org" style="margin:0px;padding:0px;border:0px;font-size:12px;vertical-align:baseline;text-decoration:initial;font-family:'Lucida Grande',LucidaGrande,Lucida,Helvetica,Arial,sans-serif" target="_blank">info@1000genomes.org</a></div>
<div><br></div><div>Documentation for the script is here: <a href="http://www.1000genomes.org/variation-pattern-finder" target="_blank">http://www.1000genomes.org/variation-pattern-finder</a></div><div><br></div><div>
Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On 20 February 2013 11:11, Nick England <span dir="ltr"><<a href="mailto:nickengland@gmail.com" target="_blank">nickengland@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">Hello all,<br><br>I hope this is the correct place to ask. I am trying to use the Variant Pattern Finder perl script (<a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/variation_pattern_finder/version_1.0/variant_pattern_finder.pl" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/browser/variation_pattern_finder/version_1.0/variant_pattern_finder.pl</a>) to analyse the 1000genome data. I am getting an error message when I run it.<br>
<br>I am using a command like:<br>perl <a href="http://variant_pattern_finder.pl" target="_blank">variant_pattern_finder.pl</a> -vcf <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz</a> -sample_panel_file <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel</a><br>
<br>I am using version 69 of the Ensemble API as this seems to be the version which 1000genome is using.<br><br>and I get the error message:<br><br>Wrong number of fieldsin <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz</a>; expected 1101, got 937. The offending line was:<br>
(very long list of numbers)<br>at /home/nengland/software/perlAPI/vcftools_0.1.10/perl/Vcf.pm line 177<br> Vcf::throw('Vcf4_1=HASH(0x131fbd8)', 'Wrong number of fieldsin <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1..." target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1...</a>') called at /home/nengland/software/perlAPI/vcftools_0.1.10/perl/Vcf.pm line 508<br>
VcfReader::next_data_hash('Vcf4_1=HASH(0x131fbd8)') called at /home/nengland/software/perlAPI/vcftools_0.1.10/perl/Vcf.pm line 3393<br> Vcf4_1::next_data_hash('Vcf4_1=HASH(0x131fbd8)') called at <a href="http://variant_pattern_finder.pl" target="_blank">variant_pattern_finder.pl</a> line 105<br>
<br>The exact number seems to change, eg if I re-run it I get "expected 1101, got 455" instead of "got 937".<br><br>Any help would be appreciated!<br><br>Thanks,<br><br>Nick England<br>
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