[2024-01-25 18:59:50,832] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:50,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:50,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference
[2024-01-25 18:59:52,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:52,027] [INFO] Task started: Prodigal
[2024-01-25 18:59:52,027] [INFO] Running command: gunzip -c /var/lib/cwl/stg8485975e-dc72-41ad-aedb-3614fbf20ad2/GCF_014197445.1_ASM1419744v1_genomic.fna.gz | prodigal -d GCF_014197445.1_ASM1419744v1_genomic.fna/cds.fna -a GCF_014197445.1_ASM1419744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:58,651] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:58,651] [INFO] Task started: HMMsearch
[2024-01-25 18:59:58,651] [INFO] Running command: hmmsearch --tblout GCF_014197445.1_ASM1419744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference/reference_markers.hmm GCF_014197445.1_ASM1419744v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:58,847] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:58,848] [INFO] Found 6/6 markers.
[2024-01-25 18:59:58,870] [INFO] Query marker FASTA was written to GCF_014197445.1_ASM1419744v1_genomic.fna/markers.fasta
[2024-01-25 18:59:58,870] [INFO] Task started: Blastn
[2024-01-25 18:59:58,870] [INFO] Running command: blastn -query GCF_014197445.1_ASM1419744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference/reference_markers.fasta -out GCF_014197445.1_ASM1419744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:59,459] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:59,461] [INFO] Selected 27 target genomes.
[2024-01-25 18:59:59,462] [INFO] Target genome list was writen to GCF_014197445.1_ASM1419744v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:59,480] [INFO] Task started: fastANI
[2024-01-25 18:59:59,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg8485975e-dc72-41ad-aedb-3614fbf20ad2/GCF_014197445.1_ASM1419744v1_genomic.fna.gz --refList GCF_014197445.1_ASM1419744v1_genomic.fna/target_genomes.txt --output GCF_014197445.1_ASM1419744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:14,711] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:14,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:14,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:14,726] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:00:14,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:00:14,726] [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 hippocampi	strain=DSM 29568	GCA_014197445.1	1628250	1628250	type	True	100.0	848	850	95	conclusive
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.2896	78	850	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	77.2375	168	850	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	77.2369	165	850	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	77.1471	152	850	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	77.0865	181	850	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	76.9194	147	850	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.8036	84	850	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.7999	73	850	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.7975	58	850	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.7219	88	850	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.6205	80	850	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.5621	92	850	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	76.5074	86	850	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	76.4682	71	850	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	76.4553	58	850	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.4518	86	850	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.4451	84	850	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	76.4393	72	850	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	76.192	86	850	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.1891	93	850	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	76.0753	68	850	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	75.6028	67	850	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:14,728] [INFO] DFAST Taxonomy check result was written to GCF_014197445.1_ASM1419744v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:14,728] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:14,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:14,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference/checkm_data
[2024-01-25 19:00:14,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:14,756] [INFO] Task started: CheckM
[2024-01-25 19:00:14,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197445.1_ASM1419744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197445.1_ASM1419744v1_genomic.fna/checkm_input GCF_014197445.1_ASM1419744v1_genomic.fna/checkm_result
[2024-01-25 19:00:38,267] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:38,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:38,287] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:38,287] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:38,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197445.1_ASM1419744v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:38,288] [INFO] Task started: Blastn
[2024-01-25 19:00:38,288] [INFO] Running command: blastn -query GCF_014197445.1_ASM1419744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46a294ec-cd10-4aff-9975-71e5c3181973/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197445.1_ASM1419744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:39,123] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:39,127] [INFO] Selected 23 target genomes.
[2024-01-25 19:00:39,127] [INFO] Target genome list was writen to GCF_014197445.1_ASM1419744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:39,154] [INFO] Task started: fastANI
[2024-01-25 19:00:39,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg8485975e-dc72-41ad-aedb-3614fbf20ad2/GCF_014197445.1_ASM1419744v1_genomic.fna.gz --refList GCF_014197445.1_ASM1419744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197445.1_ASM1419744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:54,093] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:54,106] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:54,106] [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_014197445.1	s__Mesonia hippocampi	100.0	848	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003667275.1	s__Mesonia aquimarina	77.5135	159	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	77.2175	167	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.1729	90	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	77.1471	152	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCF_900141885.1	s__Mesonia phycicola	77.0865	181	850	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	76.9042	148	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.7975	58	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116665.1	s__Pustulibacterium marinum	76.777	85	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.7219	88	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	76.6616	81	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.5718	82	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900095.1	s__Salegentibacter mishustinae	76.4873	87	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900312815.1	s__Aquimarina sp900312815	76.4647	80	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543325.1	s__Lutibacter profundi	76.4553	58	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901525.1	s__Kordia antarctica	76.4518	86	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.4451	84	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003668995.1	s__Flavobacterium sp003668995	75.7646	70	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	75.735	75	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	75.5676	70	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983975.1	s__Flavobacterium sp017983975	75.4879	54	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:54,108] [INFO] GTDB search result was written to GCF_014197445.1_ASM1419744v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:54,108] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:54,112] [INFO] DFAST_QC result json was written to GCF_014197445.1_ASM1419744v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:54,112] [INFO] DFAST_QC completed!
[2024-01-25 19:00:54,112] [INFO] Total running time: 0h1m3s