Empty VCF file

[543090lee]

Hi, I am running this command. (octopus) [seichang@login2 octopus]$ octopus -R hs37d5.fa -I HG002.hs37d5.2x250_chr19_withRG_sorted_dupMark.bam -o octopus.vcf

All the bam and fasta files, and it indexes are in the same directory.

This is the vcf file ##fileformat=VCFv4.3 ##FILTER=<ID=PASS,Description="All filters passed"> ##reference=hs37d5 ##octopus_version=0.6.3-beta ##FILTER=<ID=DP,Description="Read depth around variant is low"> ##FILTER=<ID=LBQ,Description="Median base quality supporting variant is low"> ##FILTER=<ID=SB,Description="One of the alternative alleles has strand bias"> ##FILTER=<ID=AFB,Description="The called allele frequencies are not as expected for the given ploidy"> ##FILTER=<ID=MP,Description="Variant failed model posterior filter"> ##FILTER=<ID=MQ,Description="Mapping quality across calling region is low"> ##FILTER=<ID=q10,Description="Variant quality is below 10"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position for this sample"> ##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample genotype filter indicating if this genotype was 'called'"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality (phred-scaled)"> ##FORMAT=<ID=PS,Number=1,Type=String,Description="Phase set"> ##FORMAT=<ID=PQ,Number=1,Type=Integer,Description="Phasing quality"> ##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="RMS mapping quality"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined depth across samples"> ##INFO=<ID=MQ,Number=1,Type=Integer,Description="RMS mapping quality"> ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Number of MAPQ == 0 reads covering this record"> ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=MP,Number=1,Type=Float,Description="Model posterior"> ##contig=<ID=1,length=249250621> ##contig=<ID=2,length=243199373> ##contig=<ID=3,length=198022430> ##contig=<ID=4,length=191154276> ##contig=<ID=5,length=180915260> ##contig=<ID=6,length=171115067> ##contig=<ID=7,length=159138663> ##contig=<ID=8,length=146364022> ##contig=<ID=9,length=141213431> ##contig=<ID=10,length=135534747> ##contig=<ID=11,length=135006516> ##contig=<ID=12,length=133851895> ##contig=<ID=13,length=115169878> ##contig=<ID=14,length=55189080> ##octopus=<command="octopus -R hs37d5.fa -I HG002.hs37d5.2x250_chr19_withRG_sorted_dupMark.bam -o octopus.vcf"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002

Here is the output: [2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------ [2023-04-16 21:15:20] <INFO> octopus v0.6.3-beta [2023-04-16 21:15:20] <INFO> Copyright (c) 2015-2019 University of Oxford [2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------ [2023-04-16 21:15:20] <WARN> Could not estimate read size from data, resorting to default [2023-04-16 21:15:20] <INFO> Done initialising calling components in 151ms [2023-04-16 21:15:20] <INFO> Detected 1 sample: "HG002" [2023-04-16 21:15:20] <INFO> Invoked calling model: individual [2023-04-16 21:15:20] <INFO> Processing 2,255,125,259bp with a single thread (12 cores detected) [2023-04-16 21:15:20] <INFO> Writing filtered calls to "/u/home/s/seichang/octopus/octopus.vcf" [2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------ [2023-04-16 21:15:20] <INFO> current | | time | estimated
[2023-04-16 21:15:20] <INFO> position | completed | taken | ttc
[2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------ [2023-04-16 21:15:20] <INFO> - 100% 0ms - [2023-04-16 21:15:20] <INFO> Starting Call Set Refinement (CSR) filtering [2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------ [2023-04-16 21:15:20] <INFO> current | | time | estimated
[2023-04-16 21:15:20] <INFO> position | completed | taken | ttc
[2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------ [2023-04-16 21:15:20] <INFO> - 100% 5ms - [2023-04-16 21:15:20] <INFO> Finished calling 2,255,125,259bp, total runtime 47ms [2023-04-16 21:15:20] <INFO> Calls have been written to "/u/home/s/seichang/octopus/octopus.vcf" [2023-04-16 21:15:20] <INFO> Removed 2 temporary files [2023-04-16 21:15:20] <INFO> ------------------------------------------------------------------------

What is the cause of the error?

Thanks