[2024-01-25 17:44:05,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:05,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:05,593] [INFO] DQC Reference Directory: /var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference
[2024-01-25 17:44:06,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:06,730] [INFO] Task started: Prodigal
[2024-01-25 17:44:06,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg55a5c151-c815-4c9c-9f9e-d0e0349de8a3/GCF_000092845.1_ASM9284v1_genomic.fna.gz | prodigal -d GCF_000092845.1_ASM9284v1_genomic.fna/cds.fna -a GCF_000092845.1_ASM9284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:11,260] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:11,260] [INFO] Task started: HMMsearch
[2024-01-25 17:44:11,260] [INFO] Running command: hmmsearch --tblout GCF_000092845.1_ASM9284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference/reference_markers.hmm GCF_000092845.1_ASM9284v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:11,473] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:11,474] [INFO] Found 6/6 markers.
[2024-01-25 17:44:11,500] [INFO] Query marker FASTA was written to GCF_000092845.1_ASM9284v1_genomic.fna/markers.fasta
[2024-01-25 17:44:11,501] [INFO] Task started: Blastn
[2024-01-25 17:44:11,501] [INFO] Running command: blastn -query GCF_000092845.1_ASM9284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference/reference_markers.fasta -out GCF_000092845.1_ASM9284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:12,016] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:12,018] [INFO] Selected 9 target genomes.
[2024-01-25 17:44:12,019] [INFO] Target genome list was writen to GCF_000092845.1_ASM9284v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:12,027] [INFO] Task started: fastANI
[2024-01-25 17:44:12,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a5c151-c815-4c9c-9f9e-d0e0349de8a3/GCF_000092845.1_ASM9284v1_genomic.fna.gz --refList GCF_000092845.1_ASM9284v1_genomic.fna/target_genomes.txt --output GCF_000092845.1_ASM9284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:20,750] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:20,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:20,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:20,758] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:20,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:20,758] [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
Brachyspira murdochii	strain=DSM 12563	GCA_000092845.1	84378	84378	type	True	100.0	1073	1080	95	conclusive
Brachyspira innocens	strain=B256	GCA_000384655.1	13264	13264	type	True	93.1962	875	1080	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_002214805.1	1287055	1287055	type	True	86.0522	811	1080	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_001746225.1	1287055	1287055	type	True	85.9738	801	1080	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_000383255.1	159	159	type	True	83.6805	774	1080	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_001013005.1	159	159	type	True	83.6652	772	1080	95	below_threshold
Brachyspira suanatina	strain=AN4859/03	GCA_001049755.1	381802	381802	type	True	83.6608	801	1080	95	below_threshold
Brachyspira hyodysenteriae	strain=B-78	GCA_001676785.2	159	159	type	True	83.6281	778	1080	95	below_threshold
Brachyspira intermedia	strain=PWS/A	GCA_000223215.1	84377	84377	type	True	83.4669	800	1080	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:20,760] [INFO] DFAST Taxonomy check result was written to GCF_000092845.1_ASM9284v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:20,761] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:20,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:20,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference/checkm_data
[2024-01-25 17:44:20,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:20,795] [INFO] Task started: CheckM
[2024-01-25 17:44:20,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092845.1_ASM9284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092845.1_ASM9284v1_genomic.fna/checkm_input GCF_000092845.1_ASM9284v1_genomic.fna/checkm_result
[2024-01-25 17:44:39,915] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:39,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:39,937] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:39,937] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:39,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092845.1_ASM9284v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:39,938] [INFO] Task started: Blastn
[2024-01-25 17:44:39,938] [INFO] Running command: blastn -query GCF_000092845.1_ASM9284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2104415a-cc71-4c05-be34-b823e1b9178d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092845.1_ASM9284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:40,685] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:40,689] [INFO] Selected 10 target genomes.
[2024-01-25 17:44:40,689] [INFO] Target genome list was writen to GCF_000092845.1_ASM9284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:40,697] [INFO] Task started: fastANI
[2024-01-25 17:44:40,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg55a5c151-c815-4c9c-9f9e-d0e0349de8a3/GCF_000092845.1_ASM9284v1_genomic.fna.gz --refList GCF_000092845.1_ASM9284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092845.1_ASM9284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:50,554] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:50,561] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:50,561] [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
GCF_000092845.1	s__Brachyspira murdochii	100.0	1076	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	97.81	96.97	0.94	0.93	3	conclusive
GCF_000384655.1	s__Brachyspira innocens	93.2092	873	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379365.1	s__Brachyspira sp002379365	92.4755	903	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214805.1	s__Brachyspira hampsonii	86.0431	810	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.94	99.90	1.00	1.00	3	-
GCF_001746205.1	s__Brachyspira hampsonii_B	86.0182	820	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316195.1	s__Brachyspira hampsonii_C	85.7339	780	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.70	97.44	0.97	0.94	3	-
GCF_001049755.1	s__Brachyspira suanatina	83.6502	803	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676785.2	s__Brachyspira hyodysenteriae	83.6496	774	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.16	98.93	0.98	0.95	58	-
GCF_000223215.1	s__Brachyspira intermedia	83.4683	800	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578695.1	s__Brachyspira sp910578695	82.3134	659	1080	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:50,562] [INFO] GTDB search result was written to GCF_000092845.1_ASM9284v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:50,563] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:50,566] [INFO] DFAST_QC result json was written to GCF_000092845.1_ASM9284v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:50,566] [INFO] DFAST_QC completed!
[2024-01-25 17:44:50,566] [INFO] Total running time: 0h0m45s