[2024-01-24 14:15:29,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:29,148] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:29,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference
[2024-01-24 14:15:30,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:30,376] [INFO] Task started: Prodigal
[2024-01-24 14:15:30,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgf97c7c9c-f2a1-452a-b73f-7e929a35ccd0/GCF_014651475.1_ASM1465147v1_genomic.fna.gz | prodigal -d GCF_014651475.1_ASM1465147v1_genomic.fna/cds.fna -a GCF_014651475.1_ASM1465147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:40,651] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:40,651] [INFO] Task started: HMMsearch
[2024-01-24 14:15:40,651] [INFO] Running command: hmmsearch --tblout GCF_014651475.1_ASM1465147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference/reference_markers.hmm GCF_014651475.1_ASM1465147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:40,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:40,868] [INFO] Found 6/6 markers.
[2024-01-24 14:15:40,896] [INFO] Query marker FASTA was written to GCF_014651475.1_ASM1465147v1_genomic.fna/markers.fasta
[2024-01-24 14:15:40,896] [INFO] Task started: Blastn
[2024-01-24 14:15:40,896] [INFO] Running command: blastn -query GCF_014651475.1_ASM1465147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference/reference_markers.fasta -out GCF_014651475.1_ASM1465147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:41,598] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:41,601] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:41,602] [INFO] Target genome list was writen to GCF_014651475.1_ASM1465147v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:41,616] [INFO] Task started: fastANI
[2024-01-24 14:15:41,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgf97c7c9c-f2a1-452a-b73f-7e929a35ccd0/GCF_014651475.1_ASM1465147v1_genomic.fna.gz --refList GCF_014651475.1_ASM1465147v1_genomic.fna/target_genomes.txt --output GCF_014651475.1_ASM1465147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:50,918] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:50,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:50,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:50,931] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:50,931] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:50,931] [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
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	100.0	1037	1038	95	conclusive
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	99.984	1023	1038	95	conclusive
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	81.2883	695	1038	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	81.0966	581	1038	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	79.1185	257	1038	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	78.0431	233	1038	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	77.8926	305	1038	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.814	167	1038	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.7618	101	1038	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.5848	68	1038	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	76.4736	87	1038	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.3113	58	1038	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	76.0995	96	1038	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.0194	95	1038	95	below_threshold
Mesohalobacter halotolerans	strain=WDS2C27	GCA_006120725.1	1883405	1883405	type	True	75.7736	62	1038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:50,933] [INFO] DFAST Taxonomy check result was written to GCF_014651475.1_ASM1465147v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:50,934] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:50,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:50,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference/checkm_data
[2024-01-24 14:15:50,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:50,969] [INFO] Task started: CheckM
[2024-01-24 14:15:50,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651475.1_ASM1465147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651475.1_ASM1465147v1_genomic.fna/checkm_input GCF_014651475.1_ASM1465147v1_genomic.fna/checkm_result
[2024-01-24 14:16:24,044] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:24,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:24,061] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:24,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:24,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651475.1_ASM1465147v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:24,062] [INFO] Task started: Blastn
[2024-01-24 14:16:24,062] [INFO] Running command: blastn -query GCF_014651475.1_ASM1465147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1715e37e-d3f8-46ef-a8f1-712dd0316636/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651475.1_ASM1465147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:24,984] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:24,987] [INFO] Selected 9 target genomes.
[2024-01-24 14:16:24,988] [INFO] Target genome list was writen to GCF_014651475.1_ASM1465147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:25,002] [INFO] Task started: fastANI
[2024-01-24 14:16:25,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgf97c7c9c-f2a1-452a-b73f-7e929a35ccd0/GCF_014651475.1_ASM1465147v1_genomic.fna.gz --refList GCF_014651475.1_ASM1465147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651475.1_ASM1465147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:32,102] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:32,111] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:32,111] [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_000423405.1	s__Mesonia mobilis	99.984	1023	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_012964435.1	s__Mesonia sp012964435	92.1265	771	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_008692195.1	s__Mesonia sp008692195	84.8844	726	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499555.1	s__Mesonia oceanica	81.3014	694	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_900141885.1	s__Mesonia phycicola	81.09	580	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667275.1	s__Mesonia aquimarina	79.4178	394	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	79.1371	256	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	78.4184	89	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	77.8977	306	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:32,113] [INFO] GTDB search result was written to GCF_014651475.1_ASM1465147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:32,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:32,116] [INFO] DFAST_QC result json was written to GCF_014651475.1_ASM1465147v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:32,116] [INFO] DFAST_QC completed!
[2024-01-24 14:16:32,116] [INFO] Total running time: 0h1m3s