[2024-01-25 18:14:05,718] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:05,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:05,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference
[2024-01-25 18:14:06,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:06,934] [INFO] Task started: Prodigal
[2024-01-25 18:14:06,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg975092b0-1ab0-47fd-8d97-e1ebc1421eaa/GCF_014596975.1_ASM1459697v1_genomic.fna.gz | prodigal -d GCF_014596975.1_ASM1459697v1_genomic.fna/cds.fna -a GCF_014596975.1_ASM1459697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:17,236] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:17,237] [INFO] Task started: HMMsearch
[2024-01-25 18:14:17,237] [INFO] Running command: hmmsearch --tblout GCF_014596975.1_ASM1459697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference/reference_markers.hmm GCF_014596975.1_ASM1459697v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:17,450] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:17,451] [INFO] Found 6/6 markers.
[2024-01-25 18:14:17,484] [INFO] Query marker FASTA was written to GCF_014596975.1_ASM1459697v1_genomic.fna/markers.fasta
[2024-01-25 18:14:17,485] [INFO] Task started: Blastn
[2024-01-25 18:14:17,485] [INFO] Running command: blastn -query GCF_014596975.1_ASM1459697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference/reference_markers.fasta -out GCF_014596975.1_ASM1459697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:18,122] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:18,126] [INFO] Selected 14 target genomes.
[2024-01-25 18:14:18,126] [INFO] Target genome list was writen to GCF_014596975.1_ASM1459697v1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:18,132] [INFO] Task started: fastANI
[2024-01-25 18:14:18,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg975092b0-1ab0-47fd-8d97-e1ebc1421eaa/GCF_014596975.1_ASM1459697v1_genomic.fna.gz --refList GCF_014596975.1_ASM1459697v1_genomic.fna/target_genomes.txt --output GCF_014596975.1_ASM1459697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:28,705] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:28,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:28,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:28,715] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:14:28,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:14:28,715] [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
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	100.0	1233	1234	95	conclusive
Aestuariibaculum suncheonense	strain=SC17	GCA_014596935.1	1028745	1028745	type	True	85.0003	892	1234	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	81.2511	679	1234	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.4416	399	1234	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.4253	392	1234	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.1918	343	1234	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.1405	296	1234	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.1178	336	1234	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.0045	333	1234	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	77.8195	238	1234	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.7308	183	1234	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.6206	280	1234	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.5548	243	1234	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.321	233	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:28,723] [INFO] DFAST Taxonomy check result was written to GCF_014596975.1_ASM1459697v1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:28,723] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:28,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:28,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference/checkm_data
[2024-01-25 18:14:28,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:28,773] [INFO] Task started: CheckM
[2024-01-25 18:14:28,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014596975.1_ASM1459697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014596975.1_ASM1459697v1_genomic.fna/checkm_input GCF_014596975.1_ASM1459697v1_genomic.fna/checkm_result
[2024-01-25 18:15:01,307] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:01,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:01,329] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:01,329] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:01,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014596975.1_ASM1459697v1_genomic.fna/markers.fasta)
[2024-01-25 18:15:01,329] [INFO] Task started: Blastn
[2024-01-25 18:15:01,329] [INFO] Running command: blastn -query GCF_014596975.1_ASM1459697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4991a806-70e8-444f-b8d3-e2473d4baa1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014596975.1_ASM1459697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:02,325] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:02,328] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:02,328] [INFO] Target genome list was writen to GCF_014596975.1_ASM1459697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:02,341] [INFO] Task started: fastANI
[2024-01-25 18:15:02,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg975092b0-1ab0-47fd-8d97-e1ebc1421eaa/GCF_014596975.1_ASM1459697v1_genomic.fna.gz --refList GCF_014596975.1_ASM1459697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014596975.1_ASM1459697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:14,340] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:14,349] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:14,349] [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_014596975.1	s__Aestuariibaculum marinum	100.0	1233	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014596935.1	s__Aestuariibaculum suncheonense	85.012	891	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596945.1	s__Aestuariibaculum sediminum	81.2578	678	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aestuariibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	79.0121	405	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	78.8983	394	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.455	397	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.2796	369	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.252	314	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.1378	387	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	78.0308	358	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723205.1	s__Formosa agariphila	77.7977	241	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.7675	220	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.6394	261	1234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:14,352] [INFO] GTDB search result was written to GCF_014596975.1_ASM1459697v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:14,353] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:14,355] [INFO] DFAST_QC result json was written to GCF_014596975.1_ASM1459697v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:14,355] [INFO] DFAST_QC completed!
[2024-01-25 18:15:14,356] [INFO] Total running time: 0h1m9s