[2024-01-24 10:47:10,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference
[2024-01-24 10:47:12,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,078] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg729ca751-da68-4790-932b-b6a32bd80894/GCF_020734085.1_ASM2073408v1_genomic.fna.gz | prodigal -d GCF_020734085.1_ASM2073408v1_genomic.fna/cds.fna -a GCF_020734085.1_ASM2073408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,542] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,542] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,542] [INFO] Running command: hmmsearch --tblout GCF_020734085.1_ASM2073408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference/reference_markers.hmm GCF_020734085.1_ASM2073408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,848] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,896] [INFO] Query marker FASTA was written to GCF_020734085.1_ASM2073408v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,896] [INFO] Task started: Blastn
[2024-01-24 10:47:23,896] [INFO] Running command: blastn -query GCF_020734085.1_ASM2073408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference/reference_markers.fasta -out GCF_020734085.1_ASM2073408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:24,501] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:24,504] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:24,505] [INFO] Target genome list was writen to GCF_020734085.1_ASM2073408v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,154] [INFO] Task started: fastANI
[2024-01-24 10:47:25,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg729ca751-da68-4790-932b-b6a32bd80894/GCF_020734085.1_ASM2073408v1_genomic.fna.gz --refList GCF_020734085.1_ASM2073408v1_genomic.fna/target_genomes.txt --output GCF_020734085.1_ASM2073408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:38,465] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:38,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:38,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:38,470] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:38,470] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:38,470] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Zhenpiania hominis	strain=BX12	GCA_014333425.1	2763644	2763644	type	True	78.4592	242	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:38,472] [INFO] DFAST Taxonomy check result was written to GCF_020734085.1_ASM2073408v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:38,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:38,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:38,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference/checkm_data
[2024-01-24 10:47:38,475] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:38,524] [INFO] Task started: CheckM
[2024-01-24 10:47:38,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020734085.1_ASM2073408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020734085.1_ASM2073408v1_genomic.fna/checkm_input GCF_020734085.1_ASM2073408v1_genomic.fna/checkm_result
[2024-01-24 10:48:16,807] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:16,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,834] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:16,835] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:16,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020734085.1_ASM2073408v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:16,836] [INFO] Task started: Blastn
[2024-01-24 10:48:16,836] [INFO] Running command: blastn -query GCF_020734085.1_ASM2073408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1617c561-dde2-4225-8089-0922efbd2d92/dqc_reference/reference_markers_gtdb.fasta -out GCF_020734085.1_ASM2073408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:17,752] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:17,755] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:17,756] [INFO] Target genome list was writen to GCF_020734085.1_ASM2073408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:17,768] [INFO] Task started: fastANI
[2024-01-24 10:48:17,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg729ca751-da68-4790-932b-b6a32bd80894/GCF_020734085.1_ASM2073408v1_genomic.fna.gz --refList GCF_020734085.1_ASM2073408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020734085.1_ASM2073408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:25,028] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,037] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:25,038] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902363595.1	s__BX12 sp902363595	98.9357	1319	1438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BX12	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014333425.1	s__BX12 sp014333425	78.4592	242	1438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BX12	95.0	98.83	98.83	0.97	0.97	2	-
GCA_910575405.1	s__BX12 sp910575405	78.0963	273	1438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BX12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911365.1	s__BX12 sp009911365	77.7991	228	1438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BX12	95.0	99.17	99.17	0.92	0.92	2	-
GCA_910583765.1	s__BX12 sp910583765	77.7193	223	1438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__BX12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,039] [INFO] GTDB search result was written to GCF_020734085.1_ASM2073408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:25,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:25,042] [INFO] DFAST_QC result json was written to GCF_020734085.1_ASM2073408v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:25,042] [INFO] DFAST_QC completed!
[2024-01-24 10:48:25,042] [INFO] Total running time: 0h1m15s