Open 543090lee opened 1 year ago
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
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
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=
reference=hs37d5
octopus_version=0.6.3-beta
FILTER=
FILTER=
FILTER=
FILTER=
FILTER=
FILTER=
FILTER=
FORMAT=
FORMAT=
FORMAT=
FORMAT=
FORMAT=
FORMAT=
FORMAT=
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
INFO=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
contig=
octopus=
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 position | completed | taken | ttc ------------------------------------------------------------------------
[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 position | completed | taken | ttc ------------------------------------------------------------------------
[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] ------------------------------------------------------------------------
[2023-04-16 21:15:20]
[2023-04-16 21:15:20]
[2023-04-16 21:15:20]
[2023-04-16 21:15:20]
What is the cause of the error?
Thanks