[2024-01-24 11:34:42,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference
[2024-01-24 11:34:43,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:43,669] [INFO] Task started: Prodigal
[2024-01-24 11:34:43,669] [INFO] Running command: gunzip -c /var/lib/cwl/stge88e1a9e-4a75-49d6-a5f3-c26464197841/GCF_021491425.1_ASM2149142v1_genomic.fna.gz | prodigal -d GCF_021491425.1_ASM2149142v1_genomic.fna/cds.fna -a GCF_021491425.1_ASM2149142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:13,942] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:13,942] [INFO] Task started: HMMsearch
[2024-01-24 11:35:13,942] [INFO] Running command: hmmsearch --tblout GCF_021491425.1_ASM2149142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference/reference_markers.hmm GCF_021491425.1_ASM2149142v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:14,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:14,263] [INFO] Found 6/6 markers.
[2024-01-24 11:35:14,310] [INFO] Query marker FASTA was written to GCF_021491425.1_ASM2149142v1_genomic.fna/markers.fasta
[2024-01-24 11:35:14,310] [INFO] Task started: Blastn
[2024-01-24 11:35:14,311] [INFO] Running command: blastn -query GCF_021491425.1_ASM2149142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference/reference_markers.fasta -out GCF_021491425.1_ASM2149142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:14,935] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:14,938] [INFO] Selected 29 target genomes.
[2024-01-24 11:35:14,939] [INFO] Target genome list was writen to GCF_021491425.1_ASM2149142v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:14,946] [INFO] Task started: fastANI
[2024-01-24 11:35:14,947] [INFO] Running command: fastANI --query /var/lib/cwl/stge88e1a9e-4a75-49d6-a5f3-c26464197841/GCF_021491425.1_ASM2149142v1_genomic.fna.gz --refList GCF_021491425.1_ASM2149142v1_genomic.fna/target_genomes.txt --output GCF_021491425.1_ASM2149142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:39,224] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:39,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:39,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:39,246] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:39,247] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:39,247] [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
Mariniradius saccharolyticus	strain=AK6	GCA_000330725.2	1245591	1245591	type	True	96.1012	1411	1557	95	conclusive
Cecembia calidifontis	strain=DSM 21411	GCA_004216715.1	1187080	1187080	type	True	76.8512	163	1557	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	76.7953	132	1557	95	below_threshold
Aquiflexum aquatile	strain=Z0201	GCA_003316845.1	2249427	2249427	type	True	76.7866	281	1557	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.7153	74	1557	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	76.6762	205	1557	95	below_threshold
Mongoliitalea lutea	strain=KCTC 23224	GCA_014652135.1	849756	849756	type	True	76.4769	101	1557	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	76.3459	59	1557	95	below_threshold
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	76.2472	91	1557	95	below_threshold
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	76.2363	54	1557	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	76.2036	78	1557	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	76.2018	76	1557	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	76.1806	107	1557	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	76.0888	58	1557	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	76.0644	76	1557	95	below_threshold
Rhodonellum psychrophilum	strain=GCM71	GCA_000473765.1	336828	336828	type	True	76.005	123	1557	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	75.9996	129	1557	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	75.9812	95	1557	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	75.8593	73	1557	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	75.8336	53	1557	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:39,248] [INFO] DFAST Taxonomy check result was written to GCF_021491425.1_ASM2149142v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:39,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:39,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:39,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference/checkm_data
[2024-01-24 11:35:39,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:39,294] [INFO] Task started: CheckM
[2024-01-24 11:35:39,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021491425.1_ASM2149142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021491425.1_ASM2149142v1_genomic.fna/checkm_input GCF_021491425.1_ASM2149142v1_genomic.fna/checkm_result
[2024-01-24 11:36:59,222] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:59,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:59,241] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:59,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:59,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021491425.1_ASM2149142v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:59,242] [INFO] Task started: Blastn
[2024-01-24 11:36:59,242] [INFO] Running command: blastn -query GCF_021491425.1_ASM2149142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70271db3-792a-4100-882e-a535431e41bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021491425.1_ASM2149142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:00,038] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:00,042] [INFO] Selected 25 target genomes.
[2024-01-24 11:37:00,042] [INFO] Target genome list was writen to GCF_021491425.1_ASM2149142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:00,054] [INFO] Task started: fastANI
[2024-01-24 11:37:00,054] [INFO] Running command: fastANI --query /var/lib/cwl/stge88e1a9e-4a75-49d6-a5f3-c26464197841/GCF_021491425.1_ASM2149142v1_genomic.fna.gz --refList GCF_021491425.1_ASM2149142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021491425.1_ASM2149142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:21,545] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:21,574] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:21,574] [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_000330725.2	s__Mariniradius saccharolyticus	96.0928	1412	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mariniradius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004216715.1	s__Cecembia calidifontis	76.8512	163	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	76.7953	132	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	76.7703	283	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354735.1	s__SW124 sp015354735	76.7429	88	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__SW124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.6971	203	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.5856	122	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	76.5068	60	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	76.4769	101	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526355.1	s__Algoriphagus marincola_A	76.4639	86	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003260975.1	s__Echinicola strongylocentroti	76.3064	83	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593605.1	s__Algoriphagus sanaruensis	76.2472	91	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807035.1	s__Algoriphagus formosus	76.2036	78	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_000325705.1	s__Echinicola vietnamensis	76.2018	76	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	76.1806	107	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	76.0888	58	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000381545.1	s__Rhodonellum psychrophilum	75.9996	129	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004571135.1	s__Algoriphagus kandeliae	75.9812	95	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	75.8593	73	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	75.8336	53	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	75.7243	53	1557	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:21,576] [INFO] GTDB search result was written to GCF_021491425.1_ASM2149142v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:21,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:21,580] [INFO] DFAST_QC result json was written to GCF_021491425.1_ASM2149142v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:21,580] [INFO] DFAST_QC completed!
[2024-01-24 11:37:21,580] [INFO] Total running time: 0h2m39s