[2023-06-04 21:24:59,321] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:24:59,324] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:24:59,324] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference
[2023-06-04 21:25:00,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:25:00,587] [INFO] Task started: Prodigal
[2023-06-04 21:25:00,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg77622456-5fb2-41c4-a13d-fd84e0c11e8f/GCA_001800975.1_ASM180097v1_genomic.fna.gz | prodigal -d GCA_001800975.1_ASM180097v1_genomic.fna/cds.fna -a GCA_001800975.1_ASM180097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:25:15,552] [INFO] Task succeeded: Prodigal
[2023-06-04 21:25:15,552] [INFO] Task started: HMMsearch
[2023-06-04 21:25:15,552] [INFO] Running command: hmmsearch --tblout GCA_001800975.1_ASM180097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference/reference_markers.hmm GCA_001800975.1_ASM180097v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:25:15,867] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:25:15,869] [INFO] Found 6/6 markers.
[2023-06-04 21:25:15,900] [INFO] Query marker FASTA was written to GCA_001800975.1_ASM180097v1_genomic.fna/markers.fasta
[2023-06-04 21:25:15,900] [INFO] Task started: Blastn
[2023-06-04 21:25:15,900] [INFO] Running command: blastn -query GCA_001800975.1_ASM180097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference/reference_markers.fasta -out GCA_001800975.1_ASM180097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:25:16,581] [INFO] Task succeeded: Blastn
[2023-06-04 21:25:16,587] [INFO] Selected 22 target genomes.
[2023-06-04 21:25:16,587] [INFO] Target genome list was writen to GCA_001800975.1_ASM180097v1_genomic.fna/target_genomes.txt
[2023-06-04 21:25:16,639] [INFO] Task started: fastANI
[2023-06-04 21:25:16,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg77622456-5fb2-41c4-a13d-fd84e0c11e8f/GCA_001800975.1_ASM180097v1_genomic.fna.gz --refList GCA_001800975.1_ASM180097v1_genomic.fna/target_genomes.txt --output GCA_001800975.1_ASM180097v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:25:31,129] [INFO] Task succeeded: fastANI
[2023-06-04 21:25:31,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:25:31,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:25:31,150] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:25:31,150] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:25:31,151] [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
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	78.1331	353	1134	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	77.9963	356	1134	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	77.9626	347	1134	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	77.9486	350	1134	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	77.8004	303	1134	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	77.6872	291	1134	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	77.1914	251	1134	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	76.4944	89	1134	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.4603	74	1134	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.4352	106	1134	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.3651	92	1134	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	76.3431	86	1134	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.3429	102	1134	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.3082	103	1134	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.2254	69	1134	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.1835	108	1134	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.1453	71	1134	95	below_threshold
Mangrovimonas xylaniphaga	strain=ST2L12	GCA_001280435.1	1645915	1645915	type	True	76.1066	53	1134	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	75.9271	65	1134	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	75.8573	54	1134	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	75.8319	77	1134	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	75.5695	53	1134	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:25:31,153] [INFO] DFAST Taxonomy check result was written to GCA_001800975.1_ASM180097v1_genomic.fna/tc_result.tsv
[2023-06-04 21:25:31,154] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:25:31,154] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:25:31,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference/checkm_data
[2023-06-04 21:25:31,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:25:31,196] [INFO] Task started: CheckM
[2023-06-04 21:25:31,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001800975.1_ASM180097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001800975.1_ASM180097v1_genomic.fna/checkm_input GCA_001800975.1_ASM180097v1_genomic.fna/checkm_result
[2023-06-04 21:26:16,497] [INFO] Task succeeded: CheckM
[2023-06-04 21:26:16,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:26:16,537] [INFO] ===== Completeness check finished =====
[2023-06-04 21:26:16,537] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:26:16,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001800975.1_ASM180097v1_genomic.fna/markers.fasta)
[2023-06-04 21:26:16,538] [INFO] Task started: Blastn
[2023-06-04 21:26:16,538] [INFO] Running command: blastn -query GCA_001800975.1_ASM180097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e6d1b7e-f40e-4e3d-a128-844d7d813ddf/dqc_reference/reference_markers_gtdb.fasta -out GCA_001800975.1_ASM180097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:26:17,417] [INFO] Task succeeded: Blastn
[2023-06-04 21:26:17,422] [INFO] Selected 6 target genomes.
[2023-06-04 21:26:17,423] [INFO] Target genome list was writen to GCA_001800975.1_ASM180097v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:26:17,472] [INFO] Task started: fastANI
[2023-06-04 21:26:17,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg77622456-5fb2-41c4-a13d-fd84e0c11e8f/GCA_001800975.1_ASM180097v1_genomic.fna.gz --refList GCA_001800975.1_ASM180097v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001800975.1_ASM180097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:26:22,349] [INFO] Task succeeded: fastANI
[2023-06-04 21:26:22,359] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:26:22,359] [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
GCA_001800975.1	s__Lutibacter sp001800975	100.0	1132	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014859175.1	s__Lutibacter sp014859175	86.7729	655	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003516285.1	s__Lutibacter sp003516285	86.1525	724	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	97.80	97.80	0.83	0.83	2	-
GCA_010906935.1	s__Lutibacter sp010906935	85.7534	676	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842505.1	s__Lutibacter sp002842505	85.0624	695	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649745.1	s__Lutibacter sp016649745	84.2944	569	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:26:22,361] [INFO] GTDB search result was written to GCA_001800975.1_ASM180097v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:26:22,362] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:26:22,379] [INFO] DFAST_QC result json was written to GCA_001800975.1_ASM180097v1_genomic.fna/dqc_result.json
[2023-06-04 21:26:22,379] [INFO] DFAST_QC completed!
[2023-06-04 21:26:22,380] [INFO] Total running time: 0h1m23s