[2024-01-24 13:46:29,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:29,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:29,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference
[2024-01-24 13:46:30,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:30,858] [INFO] Task started: Prodigal
[2024-01-24 13:46:30,858] [INFO] Running command: gunzip -c /var/lib/cwl/stgecad5709-c9c8-4b58-9b77-6eeabc1f6642/GCF_000184705.1_ASM18470v1_genomic.fna.gz | prodigal -d GCF_000184705.1_ASM18470v1_genomic.fna/cds.fna -a GCF_000184705.1_ASM18470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:39,202] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:39,203] [INFO] Task started: HMMsearch
[2024-01-24 13:46:39,203] [INFO] Running command: hmmsearch --tblout GCF_000184705.1_ASM18470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference/reference_markers.hmm GCF_000184705.1_ASM18470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:39,446] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:39,448] [INFO] Found 6/6 markers.
[2024-01-24 13:46:39,472] [INFO] Query marker FASTA was written to GCF_000184705.1_ASM18470v1_genomic.fna/markers.fasta
[2024-01-24 13:46:39,472] [INFO] Task started: Blastn
[2024-01-24 13:46:39,472] [INFO] Running command: blastn -query GCF_000184705.1_ASM18470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference/reference_markers.fasta -out GCF_000184705.1_ASM18470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:40,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:40,147] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:40,147] [INFO] Target genome list was writen to GCF_000184705.1_ASM18470v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:40,237] [INFO] Task started: fastANI
[2024-01-24 13:46:40,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgecad5709-c9c8-4b58-9b77-6eeabc1f6642/GCF_000184705.1_ASM18470v1_genomic.fna.gz --refList GCF_000184705.1_ASM18470v1_genomic.fna/target_genomes.txt --output GCF_000184705.1_ASM18470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:50,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:50,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:50,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:50,826] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:50,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:50,827] [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
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	100.0	948	948	95	conclusive
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	84.9827	722	948	95	below_threshold
Desulfovirgula thermocuniculi	strain=DSM 16036	GCA_000429345.1	348842	348842	type	True	75.9394	67	948	95	below_threshold
Hydrogenibacillus schlegelii	strain=MA 48	GCA_001653195.1	1484	1484	type	True	75.7867	52	948	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.4028	141	948	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.3821	86	948	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.3721	112	948	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.2976	120	948	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	75.0466	184	948	95	below_threshold
Nocardioides terrae	strain=CGMCC 1.7056	GCA_900112345.1	574651	574651	type	True	74.9304	51	948	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	74.7981	191	948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:50,828] [INFO] DFAST Taxonomy check result was written to GCF_000184705.1_ASM18470v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:50,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:50,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:50,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference/checkm_data
[2024-01-24 13:46:50,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:50,861] [INFO] Task started: CheckM
[2024-01-24 13:46:50,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000184705.1_ASM18470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000184705.1_ASM18470v1_genomic.fna/checkm_input GCF_000184705.1_ASM18470v1_genomic.fna/checkm_result
[2024-01-24 13:47:23,674] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:23,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,694] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:23,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:23,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000184705.1_ASM18470v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:23,695] [INFO] Task started: Blastn
[2024-01-24 13:47:23,696] [INFO] Running command: blastn -query GCF_000184705.1_ASM18470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg359305b0-e605-473c-8d5c-2a6dfc1423d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000184705.1_ASM18470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:24,811] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:24,815] [INFO] Selected 9 target genomes.
[2024-01-24 13:47:24,815] [INFO] Target genome list was writen to GCF_000184705.1_ASM18470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:24,833] [INFO] Task started: fastANI
[2024-01-24 13:47:24,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgecad5709-c9c8-4b58-9b77-6eeabc1f6642/GCF_000184705.1_ASM18470v1_genomic.fna.gz --refList GCF_000184705.1_ASM18470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000184705.1_ASM18470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:30,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:30,161] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:30,161] [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_000184705.1	s__Thermaerobacter marianensis	100.0	948	948	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000183545.2	s__Thermaerobacter subterraneus	84.9973	721	948	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	95.08	95.08	0.91	0.91	2	-
GCF_004634385.1	s__Thermaerobacter sp004634385	84.9035	693	948	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242195.1	s__Thermaerobacter sp003242195	80.5468	344	948	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577485.1	s__RSA17 sp002919105	77.5833	232	948	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__RSA17;g__RSA17	95.0	99.68	99.68	0.97	0.97	2	-
GCA_003242505.1	s__ZC4RG38 sp003242505	76.051	136	948	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__ZC4RG38;g__ZC4RG38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112345.1	s__Nocardioides terrae	74.9276	52	948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,163] [INFO] GTDB search result was written to GCF_000184705.1_ASM18470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:30,163] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:30,167] [INFO] DFAST_QC result json was written to GCF_000184705.1_ASM18470v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:30,167] [INFO] DFAST_QC completed!
[2024-01-24 13:47:30,167] [INFO] Total running time: 0h1m1s