[2023-03-19 01:25:20,226] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:25:20,227] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:25:20,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference
[2023-03-19 01:25:21,342] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:25:21,342] [INFO] Task started: Prodigal
[2023-03-19 01:25:21,342] [INFO] Running command: cat /var/lib/cwl/stg24933d2f-141a-40f7-9fd4-083ab1e14b02/OceanDNA-b6833.fa | prodigal -d OceanDNA-b6833/cds.fna -a OceanDNA-b6833/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:25:37,746] [INFO] Task succeeded: Prodigal
[2023-03-19 01:25:37,747] [INFO] Task started: HMMsearch
[2023-03-19 01:25:37,747] [INFO] Running command: hmmsearch --tblout OceanDNA-b6833/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference/reference_markers.hmm OceanDNA-b6833/protein.faa > /dev/null
[2023-03-19 01:25:37,924] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:25:37,925] [INFO] Found 6/6 markers.
[2023-03-19 01:25:37,945] [INFO] Query marker FASTA was written to OceanDNA-b6833/markers.fasta
[2023-03-19 01:25:37,946] [INFO] Task started: Blastn
[2023-03-19 01:25:37,946] [INFO] Running command: blastn -query OceanDNA-b6833/markers.fasta -db /var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference/reference_markers.fasta -out OceanDNA-b6833/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:25:38,581] [INFO] Task succeeded: Blastn
[2023-03-19 01:25:38,583] [INFO] Selected 18 target genomes.
[2023-03-19 01:25:38,584] [INFO] Target genome list was writen to OceanDNA-b6833/target_genomes.txt
[2023-03-19 01:25:38,596] [INFO] Task started: fastANI
[2023-03-19 01:25:38,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg24933d2f-141a-40f7-9fd4-083ab1e14b02/OceanDNA-b6833.fa --refList OceanDNA-b6833/target_genomes.txt --output OceanDNA-b6833/fastani_result.tsv --threads 1
[2023-03-19 01:25:48,813] [INFO] Task succeeded: fastANI
[2023-03-19 01:25:48,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:25:48,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:25:48,825] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:25:48,825] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:25:48,825] [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
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	78.7699	331	831	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.7412	354	831	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	78.73	332	831	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.7194	314	831	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.595	317	831	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.5895	317	831	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.3471	297	831	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.3339	307	831	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.333	332	831	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	78.3165	288	831	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	78.298	299	831	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.2752	306	831	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.194	291	831	95	below_threshold
Flavobacterium sediminis	strain=MEBiC07310	GCA_003148385.1	2201181	2201181	type	True	77.7109	236	831	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	77.6969	216	831	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.4616	146	831	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.7085	80	831	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.1452	79	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:25:48,826] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6833/tc_result.tsv
[2023-03-19 01:25:48,827] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:25:48,827] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:25:48,827] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference/checkm_data
[2023-03-19 01:25:48,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:25:48,833] [INFO] Task started: CheckM
[2023-03-19 01:25:48,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6833/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6833/checkm_input OceanDNA-b6833/checkm_result
[2023-03-19 01:26:31,938] [INFO] Task succeeded: CheckM
[2023-03-19 01:26:31,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:26:31,941] [INFO] ===== Completeness check finished =====
[2023-03-19 01:26:31,941] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:26:31,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6833/markers.fasta)
[2023-03-19 01:26:31,942] [INFO] Task started: Blastn
[2023-03-19 01:26:31,942] [INFO] Running command: blastn -query OceanDNA-b6833/markers.fasta -db /var/lib/cwl/stgfbc132ee-3403-4435-bd3a-4de876df3803/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6833/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:26:32,836] [INFO] Task succeeded: Blastn
[2023-03-19 01:26:32,837] [INFO] Selected 18 target genomes.
[2023-03-19 01:26:32,837] [INFO] Target genome list was writen to OceanDNA-b6833/target_genomes_gtdb.txt
[2023-03-19 01:26:32,859] [INFO] Task started: fastANI
[2023-03-19 01:26:32,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg24933d2f-141a-40f7-9fd4-083ab1e14b02/OceanDNA-b6833.fa --refList OceanDNA-b6833/target_genomes_gtdb.txt --output OceanDNA-b6833/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:26:42,636] [INFO] Task succeeded: fastANI
[2023-03-19 01:26:42,647] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:26:42,647] [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_009363055.1	s__Flavobacterium haoranii	78.7172	333	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000967805.1	s__Flavobacterium sp000967805	78.7089	353	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	78.6835	298	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.588	317	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014763515.1	s__Flavobacterium sp014763515	78.541	196	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862755.1	s__Flavobacterium sp002862755	78.463	305	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	78.354	298	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	78.3257	332	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	78.311	298	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	78.3028	289	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	78.2701	309	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963025.1	s__Flavobacterium sp003963025	78.1597	214	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246205.1	s__Flavobacterium haoranii_A	78.1438	201	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	78.1098	297	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_004303025.1	s__Flavobacterium sp004303025	78.0871	329	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	78.059	245	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148385.1	s__Flavobacterium sediminis	77.7196	236	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455605.1	s__Flavobacterium indicum	77.712	215	831	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:26:42,647] [INFO] GTDB search result was written to OceanDNA-b6833/result_gtdb.tsv
[2023-03-19 01:26:42,647] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:26:42,649] [INFO] DFAST_QC result json was written to OceanDNA-b6833/dqc_result.json
[2023-03-19 01:26:42,650] [INFO] DFAST_QC completed!
[2023-03-19 01:26:42,650] [INFO] Total running time: 0h1m22s