[2024-01-24 14:12:02,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:02,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:02,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference
[2024-01-24 14:12:04,349] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:04,351] [INFO] Task started: Prodigal
[2024-01-24 14:12:04,352] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa614a98-f781-42fc-8835-e9e05d443a64/GCF_004364175.1_ASM436417v1_genomic.fna.gz | prodigal -d GCF_004364175.1_ASM436417v1_genomic.fna/cds.fna -a GCF_004364175.1_ASM436417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:20,249] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:20,250] [INFO] Task started: HMMsearch
[2024-01-24 14:12:20,250] [INFO] Running command: hmmsearch --tblout GCF_004364175.1_ASM436417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference/reference_markers.hmm GCF_004364175.1_ASM436417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:20,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:20,559] [INFO] Found 6/6 markers.
[2024-01-24 14:12:20,595] [INFO] Query marker FASTA was written to GCF_004364175.1_ASM436417v1_genomic.fna/markers.fasta
[2024-01-24 14:12:20,596] [INFO] Task started: Blastn
[2024-01-24 14:12:20,596] [INFO] Running command: blastn -query GCF_004364175.1_ASM436417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference/reference_markers.fasta -out GCF_004364175.1_ASM436417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:21,301] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:21,304] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:21,304] [INFO] Target genome list was writen to GCF_004364175.1_ASM436417v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:21,311] [INFO] Task started: fastANI
[2024-01-24 14:12:21,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa614a98-f781-42fc-8835-e9e05d443a64/GCF_004364175.1_ASM436417v1_genomic.fna.gz --refList GCF_004364175.1_ASM436417v1_genomic.fna/target_genomes.txt --output GCF_004364175.1_ASM436417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:32,415] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:32,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:32,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:32,426] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:32,427] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:32,427] [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
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	100.0	1418	1418	95	conclusive
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	87.3387	1157	1418	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	86.1016	1128	1418	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	85.4131	1062	1418	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	83.8993	991	1418	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	83.2998	1002	1418	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	83.1818	978	1418	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.4112	87	1418	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.7031	59	1418	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.3193	113	1418	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.1616	88	1418	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.8979	86	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:32,428] [INFO] DFAST Taxonomy check result was written to GCF_004364175.1_ASM436417v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:32,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:32,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:32,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference/checkm_data
[2024-01-24 14:12:32,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:32,473] [INFO] Task started: CheckM
[2024-01-24 14:12:32,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364175.1_ASM436417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364175.1_ASM436417v1_genomic.fna/checkm_input GCF_004364175.1_ASM436417v1_genomic.fna/checkm_result
[2024-01-24 14:13:17,719] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:17,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:17,737] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:17,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:17,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364175.1_ASM436417v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:17,738] [INFO] Task started: Blastn
[2024-01-24 14:13:17,738] [INFO] Running command: blastn -query GCF_004364175.1_ASM436417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8b08f1e-ef4a-4c1c-a535-4925ea2bc529/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364175.1_ASM436417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:18,714] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:18,718] [INFO] Selected 8 target genomes.
[2024-01-24 14:13:18,718] [INFO] Target genome list was writen to GCF_004364175.1_ASM436417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:18,727] [INFO] Task started: fastANI
[2024-01-24 14:13:18,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa614a98-f781-42fc-8835-e9e05d443a64/GCF_004364175.1_ASM436417v1_genomic.fna.gz --refList GCF_004364175.1_ASM436417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364175.1_ASM436417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:27,010] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:27,025] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:27,025] [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_004364175.1	s__Maribacter caenipelagi	100.0	1418	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142175.1	s__Maribacter aquivivus	87.3387	1157	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	86.0987	1128	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	85.4094	1062	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	83.9089	990	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_900112245.1	s__Maribacter stanieri	83.3084	1001	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900155985.1	s__Maribacter ulvicola	83.188	977	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	82.6207	956	1418	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:27,027] [INFO] GTDB search result was written to GCF_004364175.1_ASM436417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:27,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:27,033] [INFO] DFAST_QC result json was written to GCF_004364175.1_ASM436417v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:27,033] [INFO] DFAST_QC completed!
[2024-01-24 14:13:27,033] [INFO] Total running time: 0h1m24s