[2024-01-24 14:28:08,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference
[2024-01-24 14:28:10,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,419] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,420] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3b3568b-bcb7-4789-9908-70b27fe471eb/GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/cds.fna -a GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:25,940] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:25,941] [INFO] Task started: HMMsearch
[2024-01-24 14:28:25,941] [INFO] Running command: hmmsearch --tblout GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference/reference_markers.hmm GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:26,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:26,270] [INFO] Found 6/6 markers.
[2024-01-24 14:28:26,316] [INFO] Query marker FASTA was written to GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:28:26,316] [INFO] Task started: Blastn
[2024-01-24 14:28:26,317] [INFO] Running command: blastn -query GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference/reference_markers.fasta -out GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:27,114] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:27,117] [INFO] Selected 21 target genomes.
[2024-01-24 14:28:27,118] [INFO] Target genome list was writen to GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:28:27,141] [INFO] Task started: fastANI
[2024-01-24 14:28:27,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3b3568b-bcb7-4789-9908-70b27fe471eb/GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna.gz --refList GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:43,399] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:43,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:43,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:43,416] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:43,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:43,417] [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
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	100.0	1543	1543	95	conclusive
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	81.7729	692	1543	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	80.6615	610	1543	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	79.9935	544	1543	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	79.0034	394	1543	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	78.5518	294	1543	95	below_threshold
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	78.4745	360	1543	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	77.6429	238	1543	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	77.4261	121	1543	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	77.2502	167	1543	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	77.0949	150	1543	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	76.9876	88	1543	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	76.9853	128	1543	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.7307	122	1543	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	76.4248	82	1543	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	76.2943	92	1543	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	76.2639	107	1543	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	75.6341	52	1543	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	75.427	51	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:43,418] [INFO] DFAST Taxonomy check result was written to GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:28:43,419] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:43,419] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:43,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference/checkm_data
[2024-01-24 14:28:43,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:43,469] [INFO] Task started: CheckM
[2024-01-24 14:28:43,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/checkm_input GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:29:31,146] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:31,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:31,170] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:31,170] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:31,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:29:31,171] [INFO] Task started: Blastn
[2024-01-24 14:29:31,171] [INFO] Running command: blastn -query GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ceca5f7-b3a2-4f07-b8a5-fd001f6147d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:32,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:32,254] [INFO] Selected 10 target genomes.
[2024-01-24 14:29:32,254] [INFO] Target genome list was writen to GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:32,268] [INFO] Task started: fastANI
[2024-01-24 14:29:32,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3b3568b-bcb7-4789-9908-70b27fe471eb/GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna.gz --refList GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:40,893] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:40,904] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:40,904] [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_900155945.1	s__Marinobacterium stanieri	100.0	1543	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	conclusive
GCF_017776525.1	s__Marinobacterium alkalitolerans	81.794	690	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	81.0985	615	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014615.1	s__Marinobacterium halophilum	80.6588	611	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.87	98.87	0.91	0.91	2	-
GCF_013868415.1	s__Marinobacterium sp013868415	80.5552	491	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107855.1	s__Marinobacterium georgiense	80.0171	540	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.23	97.23	0.75	0.75	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	79.0311	391	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	77.612	292	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178375.1	s__Ch67 sp013178375	76.4418	91	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Ketobacteraceae;g__Ch67	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298335.1	s__Oleibacter sp002298335	76.4031	91	1543	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	99.94	99.90	0.96	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:40,906] [INFO] GTDB search result was written to GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:40,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:40,910] [INFO] DFAST_QC result json was written to GCF_900155945.1_IMG-taxon_2681813548_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:29:40,910] [INFO] DFAST_QC completed!
[2024-01-24 14:29:40,910] [INFO] Total running time: 0h1m32s