<p>Oh this is fairly easy. The file size has exceed the capacity of Excel (50000 rows??). This doesn't affect downstream analysis because the rows are there you just can't visualise them.</p>
<p><strong>BBEdit</strong> will open it if this is Mac (free from AppStore - really good BTW). If this is Linux then <code>vi</code> or <code>vim</code>. A Windows version of BBEdit is <strong>Notepad++</strong>, please not Notepad.</p>
<p>You can request the number of lines (bash Linux) via</p>
<pre><code>wc weir.fst 
</code></pre>
<p>This will return the number of lines in the file, if it's &gt;50000, i.e. beyond the number of the Excel limit, that's your answer. You just need to find an alternative viewer</p>

CC BY-SA 4.0
2023-07-17T08:42:23.083Z
Thank you. Now I am really embaresed, that I opened those files in that way.
Lukas Chumchal
CC BY-SA 4.0
2023-07-16T00:10:44.227Z
2023-07-16T00:10:44.227Z
M__
<p>I have .vcf file with over 78 000 variations in 95 experiment subjects. I used vcftools to extract fixation index score for general differentiation between Case and Control groups.</p>
<pre><code>./vcftools --vcf SCH_freebayes_sort_ostE_SnpEff_SnpSift.vcf --weir-fst-pop Case.txt --weir-fst-pop Control.txt --out FstExon_Case_vs_Control
</code></pre>
<pre><code>VCFtools - 0.1.17
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf SCH_freebayes_sort_ostE_SnpEff_SnpSift.vcf
    --weir-fst-pop Case.txt
    --weir-fst-pop Control.txt
    --keep Case.txt
    --keep Control.txt
    --out Fst_TestData_nochange

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description=&quot;Estimated allele frequency in the range (0,1]&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=PRO,Number=1,Type=Float,Description=&quot;Reference allele observation count, with partial observations recorded fractionally&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=PAO,Number=A,Type=Float,Description=&quot;Alternate allele observations, with partial observations recorded fractionally&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SRP,Number=1,Type=Float,Description=&quot;Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SAP,Number=A,Type=Float,Description=&quot;Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=AB,Number=A,Type=Float,Description=&quot;Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=ABP,Number=A,Type=Float,Description=&quot;Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=RPP,Number=A,Type=Float,Description=&quot;Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=RPPR,Number=1,Type=Float,Description=&quot;Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=EPP,Number=A,Type=Float,Description=&quot;End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=EPPR,Number=1,Type=Float,Description=&quot;End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description=&quot;The type of allele, either snp, mnp, ins, del, or complex.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description=&quot;The type of allele, either snp, mnp, ins, del, or complex.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description=&quot;The type of allele, either snp, mnp, ins, del, or complex.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description=&quot;The type of allele, either snp, mnp, ins, del, or complex.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description=&quot;The type of allele, either snp, mnp, ins, del, or complex.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=CIGAR,Number=A,Type=String,Description=&quot;The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.&quot;&gt;
Warning: Expected at least 2 parts in FORMAT entry: ID=GQ,Number=1,Type=Float,Description=&quot;Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype&quot;&gt;
Warning: Expected at least 2 parts in FORMAT entry: ID=GL,Number=G,Type=Float,Description=&quot;Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=WTD,Number=0,Type=Flag,Description=&quot;Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set.  If all member ss' are withdrawn, then the rs is deleted to SNPHistory&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=WTD,Number=0,Type=Flag,Description=&quot;Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set.  If all member ss' are withdrawn, then the rs is deleted to SNPHistory&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TOPMED,Number=.,Type=String,Description=&quot;An ordered, comma delimited list of allele frequencies based on TOPMed, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMed minor allele is the second largest value in the list.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=TOPMED,Number=.,Type=String,Description=&quot;An ordered, comma delimited list of allele frequencies based on TOPMed, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMed minor allele is the second largest value in the list.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description=&quot;Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description=&quot;Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description=&quot;Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description=&quot;Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=MTP,Number=0,Type=Flag,Description=&quot;Microattribution/third-party annotation(TPA:GWAS,PAGE)&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=NOC,Number=0,Type=Flag,Description=&quot;Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation.&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description=&quot;An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description=&quot;An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description=&quot;An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description=&quot;An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=MUT,Number=0,Type=Flag,Description=&quot;Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SAO,Number=1,Type=Integer,Description=&quot;Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SAO,Number=1,Type=Integer,Description=&quot;Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SAO,Number=1,Type=Integer,Description=&quot;Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description=&quot;Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description=&quot;Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description=&quot;Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description=&quot;Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description=&quot;Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description=&quot;Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=PM,Number=0,Type=Flag,Description=&quot;Variant is Precious(Clinical,Pubmed Cited)&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=AF_popmax,Number=A,Type=Float,Description=&quot;Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry)&quot;&gt;
Warning: Expected at least 2 parts in INFO entry: ID=AF_popmax,Number=A,Type=Float,Description=&quot;Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry)&quot;&gt;
Keeping individuals in 'keep' list
After filtering, kept 95 out of 95 Individuals
Outputting Weir and Cockerham Fst estimates.
    Fst: Only using diploid sites.
Weir and Cockerham mean Fst estimate: -0.00031927
Weir and Cockerham weighted Fst estimate: -0.00047509
After filtering, kept 78758 out of a possible 78758 Sites
Run Time = 4.00 seconds


</code></pre>
<p>But when I tried to open .weir.fst files with notepad or excel, I lost over 9 000 rows of data. I am sure that there is problem with how I am opening the .weir.fst files.</p>
<p>Please, how are these files opened properly?</p>

CC BY-SA 4.0
2023-07-12T16:12:11.167Z
Please format your error message/console output properly.
Ram RS
CC BY-SA 4.0
2023-07-12T17:08:49.603Z
@RamRS I added full log file. Please If you want to help me with formatting my question, be more direct.
Lukas Chumchal
CC BY-SA 4.0
2023-07-13T14:24:17.123Z
I was as direct as can be. What do you think I should do differently?
Ram RS
CC BY-SA 4.0
2023-07-13T17:29:54.473Z
@RamRS I apologise for my comment. I did not mean to offend you. I was only seriously frustrated and I felt hopeless. This problem took me hours. I do not know, where I made mistake.
Lukas Chumchal
CC BY-SA 4.0
2023-07-13T17:59:31.100Z
I'm not offended, Lukas. I was just wondering what I could have done differently.
Ram RS
CC BY-SA 4.0
2023-07-13T18:00:21.063Z
Also, don't open files with notepad or Excel, try unix utilities or if you're on Windows, try notepad++
Ram RS
CC BY-SA 4.0
2023-07-13T18:05:46.047Z
@RamRS Sorry, but I am new contributor. You can tell mi dircetly that I could my log message post fully and edit it little more. But still this is just pointless semantics.
Lukas Chumchal
CC BY-SA 4.0
2023-07-17T08:43:10.430Z
@RamRS Thank you.
Lukas Chumchal
<phylogenetics><phylogeny><vcftools><population-genetics><fst>
How to open .weir.fst files witout losing data?
# How to open .weir.fst files witout losing data?

(Asked by: username_0 on 2023-07-12)

I have .vcf file with over 78 000 variations in 95 experiment subjects. I used vcftools to extract fixation index score for general differentiation between Case and Control groups.
./vcftools --vcf SCH_freebayes_sort_ostE_SnpEff_SnpSift.vcf --weir-fst-pop Case.txt --weir-fst-pop Control.txt --out FstExon_Case_vs_Control

VCFtools - 0.1.17
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf SCH_freebayes_sort_ostE_SnpEff_SnpSift.vcf
    --weir-fst-pop Case.txt
    --weir-fst-pop Control.txt
    --keep Case.txt
    --keep Control.txt
    --out Fst_TestData_nochange

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
Warning: Expected at least 2 parts in INFO entry: ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
Warning: Expected at least 2 parts in INFO entry: ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
Warning: Expected at least 2 parts in INFO entry: ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
Warning: Expected at least 2 parts in INFO entry: ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
Warning: Expected at least 2 parts in FORMAT entry: ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
Warning: Expected at least 2 parts in FORMAT entry: ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
Warning: Expected at least 2 parts in INFO entry: ID=WTD,Number=0,Type=Flag,Description="Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set.  If all member ss' are withdrawn, then the rs is deleted to SNPHistory">
Warning: Expected at least 2 parts in INFO entry: ID=WTD,Number=0,Type=Flag,Description="Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set.  If all member ss' are withdrawn, then the rs is deleted to SNPHistory">
Warning: Expected at least 2 parts in INFO entry: ID=TOPMED,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on TOPMed, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMed minor allele is the second largest value in the list.">
Warning: Expected at least 2 parts in INFO entry: ID=TOPMED,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on TOPMed, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMed minor allele is the second largest value in the list.">
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
Warning: Expected at least 2 parts in INFO entry: ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
Warning: Expected at least 2 parts in INFO entry: ID=MTP,Number=0,Type=Flag,Description="Microattribution/third-party annotation(TPA:GWAS,PAGE)">
Warning: Expected at least 2 parts in INFO entry: ID=NOC,Number=0,Type=Flag,Description="Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation.">
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
Warning: Expected at least 2 parts in INFO entry: ID=CAF,Number=.,Type=String,Description="An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter">
Warning: Expected at least 2 parts in INFO entry: ID=MUT,Number=0,Type=Flag,Description="Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources">
Warning: Expected at least 2 parts in INFO entry: ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
Warning: Expected at least 2 parts in INFO entry: ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
Warning: Expected at least 2 parts in INFO entry: ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
Warning: Expected at least 2 parts in INFO entry: ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
Warning: Expected at least 2 parts in INFO entry: ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
Warning: Expected at least 2 parts in INFO entry: ID=AF_popmax,Number=A,Type=Float,Description="Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry)">
Warning: Expected at least 2 parts in INFO entry: ID=AF_popmax,Number=A,Type=Float,Description="Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry)">
Keeping individuals in 'keep' list
After filtering, kept 95 out of 95 Individuals
Outputting Weir and Cockerham Fst estimates.
    Fst: Only using diploid sites.
Weir and Cockerham mean Fst estimate: -0.00031927
Weir and Cockerham weighted Fst estimate: -0.00047509
After filtering, kept 78758 out of a possible 78758 Sites
Run Time = 4.00 seconds



But when I tried to open .weir.fst files with notepad or excel, I lost over 9 000 rows of data. I am sure that there is problem with how I am opening the .weir.fst files.
Please, how are these files opened properly?

**Tags:** phylogenetics, phylogeny, vcftools, population-genetics, fst
> **Comments:**
> **username_1**: Please format your error message/console output properly.  
> **username_0**: @RamRS I added full log file. Please If you want to help me with formatting my question, be more direct.  
> **username_1**: I was as direct as can be. What do you think I should do differently?  
> **username_0**: @RamRS I apologise for my comment. I did not mean to offend you. I was only seriously frustrated and I felt hopeless. This problem took me hours. I do not know, where I made mistake.  
> **username_1**: I'm not offended, Lukas. I was just wondering what I could have done differently.  
> **username_1**: Also, don't open files with notepad or Excel, try unix utilities or if you're on Windows, try notepad++  
> **username_0**: @RamRS Sorry, but I am new contributor. You can tell mi dircetly that I could my log message post fully and edit it little more. But still this is just pointless semantics.  
> **username_0**: @RamRS Thank you.  

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## 1 answers

### Answer by username_2 on 2023-07-16. Score: 1 | Accepted answer

Oh this is fairly easy. The file size has exceed the capacity of Excel (50000 rows??). This doesn't affect downstream analysis because the rows are there you just can't visualise them.
BBEdit will open it if this is Mac (free from AppStore - really good BTW). If this is Linux then vi or vim. A Windows version of BBEdit is Notepad++, please not Notepad.
You can request the number of lines (bash Linux) via
wc weir.fst 

This will return the number of lines in the file, if it's >50000, i.e. beyond the number of the Excel limit, that's your answer. You just need to find an alternative viewer

> **Comments:**
> **username_0**: Thank you. Now I am really embaresed, that I opened those files in that way.  

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