[2024-01-24 12:30:09,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:09,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:09,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference
[2024-01-24 12:30:12,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:12,007] [INFO] Task started: Prodigal
[2024-01-24 12:30:12,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f6e1761-2089-4a01-bd2b-52fd94b1920e/GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/cds.fna -a GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:23,365] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:23,365] [INFO] Task started: HMMsearch
[2024-01-24 12:30:23,365] [INFO] Running command: hmmsearch --tblout GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference/reference_markers.hmm GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:23,664] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:23,667] [INFO] Found 6/6 markers.
[2024-01-24 12:30:23,708] [INFO] Query marker FASTA was written to GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:30:23,709] [INFO] Task started: Blastn
[2024-01-24 12:30:23,709] [INFO] Running command: blastn -query GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference/reference_markers.fasta -out GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:24,466] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:24,472] [INFO] Selected 14 target genomes.
[2024-01-24 12:30:24,472] [INFO] Target genome list was writen to GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:30:24,478] [INFO] Task started: fastANI
[2024-01-24 12:30:24,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6e1761-2089-4a01-bd2b-52fd94b1920e/GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna.gz --refList GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:34,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:34,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:34,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:34,467] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:34,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:34,468] [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 oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	100.0	1347	1349	95	conclusive
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	80.8228	764	1349	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	79.8758	582	1349	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	79.6277	543	1349	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	79.6068	559	1349	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	79.5434	556	1349	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	79.2001	532	1349	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	78.3665	428	1349	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	77.557	239	1349	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.5204	273	1349	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.3825	330	1349	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.3133	234	1349	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.2742	255	1349	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.0887	277	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:34,474] [INFO] DFAST Taxonomy check result was written to GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:30:34,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:34,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:34,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference/checkm_data
[2024-01-24 12:30:34,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:34,515] [INFO] Task started: CheckM
[2024-01-24 12:30:34,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/checkm_input GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:31:12,918] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:12,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:12,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:12,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:12,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:31:12,941] [INFO] Task started: Blastn
[2024-01-24 12:31:12,942] [INFO] Running command: blastn -query GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a2eeb7b-69dc-4656-9266-901fc9128379/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:13,970] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:13,973] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:13,973] [INFO] Target genome list was writen to GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:13,988] [INFO] Task started: fastANI
[2024-01-24 12:31:13,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6e1761-2089-4a01-bd2b-52fd94b1920e/GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna.gz --refList GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:23,367] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:23,378] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:23,378] [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_900106565.1	s__Lutibacter oricola	100.0	1347	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003260195.1	s__Lutibacter citreus	80.8254	763	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	79.8889	581	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384935.1	s__Lutibacter oceani	79.5916	546	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188355.1	s__Lutibacter flavus	79.5384	556	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	79.5028	549	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004195315.1	s__Lutibacter sp004195315	79.093	313	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	79.0831	476	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	78.9303	436	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015767395.1	s__Lutibacter sp015767395	78.478	288	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687935.1	s__Polaribacter sp000687935	77.2969	270	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	77.2771	226	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:23,380] [INFO] GTDB search result was written to GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:23,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:23,385] [INFO] DFAST_QC result json was written to GCF_900106565.1_IMG-taxon_2693429896_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:31:23,386] [INFO] DFAST_QC completed!
[2024-01-24 12:31:23,386] [INFO] Total running time: 0h1m14s