Empty VCF file

[Seungmo Lee]

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

What is the cause of the error?

Thanks