[2023-03-15 16:21:34,080] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:21:34,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:21:34,081] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference
[2023-03-15 16:21:36,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:21:36,309] [INFO] Task started: Prodigal
[2023-03-15 16:21:36,309] [INFO] Running command: cat /var/lib/cwl/stg69979f24-b8f0-4672-a132-859c3f2e2b01/OceanDNA-b6850.fa | prodigal -d OceanDNA-b6850/cds.fna -a OceanDNA-b6850/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:21:50,477] [INFO] Task succeeded: Prodigal
[2023-03-15 16:21:50,477] [INFO] Task started: HMMsearch
[2023-03-15 16:21:50,477] [INFO] Running command: hmmsearch --tblout OceanDNA-b6850/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference/reference_markers.hmm OceanDNA-b6850/protein.faa > /dev/null
[2023-03-15 16:21:50,663] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:21:50,664] [INFO] Found 6/6 markers.
[2023-03-15 16:21:50,711] [INFO] Query marker FASTA was written to OceanDNA-b6850/markers.fasta
[2023-03-15 16:21:50,712] [INFO] Task started: Blastn
[2023-03-15 16:21:50,712] [INFO] Running command: blastn -query OceanDNA-b6850/markers.fasta -db /var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference/reference_markers.fasta -out OceanDNA-b6850/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:21:51,350] [INFO] Task succeeded: Blastn
[2023-03-15 16:21:51,358] [INFO] Selected 18 target genomes.
[2023-03-15 16:21:51,358] [INFO] Target genome list was writen to OceanDNA-b6850/target_genomes.txt
[2023-03-15 16:21:51,390] [INFO] Task started: fastANI
[2023-03-15 16:21:51,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg69979f24-b8f0-4672-a132-859c3f2e2b01/OceanDNA-b6850.fa --refList OceanDNA-b6850/target_genomes.txt --output OceanDNA-b6850/fastani_result.tsv --threads 1
[2023-03-15 16:22:02,222] [INFO] Task succeeded: fastANI
[2023-03-15 16:22:02,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:22:02,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:22:02,235] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:22:02,235] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:22:02,235] [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 gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	79.6188	406	779	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.9354	423	779	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.8419	384	779	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.8392	410	779	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.8289	416	779	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	78.788	385	779	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	78.7381	378	779	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	78.722	389	779	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	78.6576	375	779	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	78.6078	374	779	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.5468	360	779	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.5422	367	779	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.4856	379	779	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.38	371	779	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.3636	372	779	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	78.2536	309	779	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.2689	188	779	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.2073	134	779	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:22:02,239] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6850/tc_result.tsv
[2023-03-15 16:22:02,240] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:22:02,240] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:22:02,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference/checkm_data
[2023-03-15 16:22:02,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:22:02,334] [INFO] Task started: CheckM
[2023-03-15 16:22:02,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6850/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6850/checkm_input OceanDNA-b6850/checkm_result
[2023-03-15 16:22:40,654] [INFO] Task succeeded: CheckM
[2023-03-15 16:22:40,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:22:40,730] [INFO] ===== Completeness check finished =====
[2023-03-15 16:22:40,730] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:22:40,731] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6850/markers.fasta)
[2023-03-15 16:22:40,732] [INFO] Task started: Blastn
[2023-03-15 16:22:40,732] [INFO] Running command: blastn -query OceanDNA-b6850/markers.fasta -db /var/lib/cwl/stgc3a2c795-5089-487f-a43f-d94b4c87db05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6850/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:22:41,651] [INFO] Task succeeded: Blastn
[2023-03-15 16:22:41,652] [INFO] Selected 20 target genomes.
[2023-03-15 16:22:41,652] [INFO] Target genome list was writen to OceanDNA-b6850/target_genomes_gtdb.txt
[2023-03-15 16:22:41,928] [INFO] Task started: fastANI
[2023-03-15 16:22:41,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg69979f24-b8f0-4672-a132-859c3f2e2b01/OceanDNA-b6850.fa --refList OceanDNA-b6850/target_genomes_gtdb.txt --output OceanDNA-b6850/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:22:54,257] [INFO] Task succeeded: fastANI
[2023-03-15 16:22:54,269] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:22:54,288] [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
GCA_002862805.1	s__Flavobacterium sp002862805	98.1462	676	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422685.1	s__Flavobacterium gelidilacus	79.6437	404	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	78.951	415	779	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	78.9339	395	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_006491595.2	s__Flavobacterium jejuense	78.8395	415	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363055.1	s__Flavobacterium haoranii	78.7932	384	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004363695.1	s__Flavobacterium cheniae	78.749	377	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003497625.1	s__Flavobacterium sp003497625	78.6833	335	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_012032075.1	s__Flavobacterium sp012032075	78.6754	316	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011392075.1	s__Flavobacterium celericrescens	78.5863	375	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401995.1	s__Flavobacterium sp018401995	78.5607	282	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293845.1	s__Flavobacterium tibetense	78.5458	359	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004303025.1	s__Flavobacterium sp004303025	78.4406	387	779	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	78.3792	370	779	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	78.3742	232	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108955.1	s__Flavobacterium terrigena	78.2587	308	779	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	78.13	352	779	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	78.0712	371	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800945.1	s__Flavobacterium sp001800945	77.9321	210	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	77.575	252	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-15 16:22:54,289] [INFO] GTDB search result was written to OceanDNA-b6850/result_gtdb.tsv
[2023-03-15 16:22:54,291] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:22:54,295] [INFO] DFAST_QC result json was written to OceanDNA-b6850/dqc_result.json
[2023-03-15 16:22:54,295] [INFO] DFAST_QC completed!
[2023-03-15 16:22:54,295] [INFO] Total running time: 0h1m20s