[2023-03-18 00:58:44,624] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,296] [INFO] Running command: cat /var/lib/cwl/stg762e0bfa-44ac-4b3b-b298-7ef261c63c31/OceanDNA-b6789.fa | prodigal -d OceanDNA-b6789/cds.fna -a OceanDNA-b6789/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:58:59,788] [INFO] Task succeeded: Prodigal
[2023-03-18 00:58:59,789] [INFO] Task started: HMMsearch
[2023-03-18 00:58:59,789] [INFO] Running command: hmmsearch --tblout OceanDNA-b6789/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference/reference_markers.hmm OceanDNA-b6789/protein.faa > /dev/null
[2023-03-18 00:58:59,953] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:58:59,954] [INFO] Found 6/6 markers.
[2023-03-18 00:58:59,970] [INFO] Query marker FASTA was written to OceanDNA-b6789/markers.fasta
[2023-03-18 00:58:59,970] [INFO] Task started: Blastn
[2023-03-18 00:58:59,970] [INFO] Running command: blastn -query OceanDNA-b6789/markers.fasta -db /var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference/reference_markers.fasta -out OceanDNA-b6789/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:00,595] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:00,596] [INFO] Selected 21 target genomes.
[2023-03-18 00:59:00,597] [INFO] Target genome list was writen to OceanDNA-b6789/target_genomes.txt
[2023-03-18 00:59:00,606] [INFO] Task started: fastANI
[2023-03-18 00:59:00,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg762e0bfa-44ac-4b3b-b298-7ef261c63c31/OceanDNA-b6789.fa --refList OceanDNA-b6789/target_genomes.txt --output OceanDNA-b6789/fastani_result.tsv --threads 1
[2023-03-18 00:59:12,153] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:12,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:12,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:12,165] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:12,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:59:12,166] [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	79.1212	364	737	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	79.0755	368	737	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	78.9959	369	737	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.958	388	737	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.9551	392	737	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.9493	333	737	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.9493	333	737	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	78.901	363	737	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.8316	352	737	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.7014	319	737	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	78.6828	342	737	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	78.6789	345	737	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.6449	325	737	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	78.6249	338	737	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	78.6238	359	737	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.3768	350	737	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	78.3743	344	737	95	below_threshold
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	78.1014	283	737	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	78.07	273	737	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	77.662	220	737	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	77.1048	207	737	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:59:12,166] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6789/tc_result.tsv
[2023-03-18 00:59:12,167] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:12,167] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:12,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference/checkm_data
[2023-03-18 00:59:12,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:12,182] [INFO] Task started: CheckM
[2023-03-18 00:59:12,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6789/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6789/checkm_input OceanDNA-b6789/checkm_result
[2023-03-18 00:59:48,935] [INFO] Task succeeded: CheckM
[2023-03-18 00:59:48,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:59:48,940] [INFO] ===== Completeness check finished =====
[2023-03-18 00:59:48,940] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:59:48,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6789/markers.fasta)
[2023-03-18 00:59:48,941] [INFO] Task started: Blastn
[2023-03-18 00:59:48,941] [INFO] Running command: blastn -query OceanDNA-b6789/markers.fasta -db /var/lib/cwl/stgb12ecfdb-0034-4f80-9acb-cb0d704c5691/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6789/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:49,877] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:49,880] [INFO] Selected 23 target genomes.
[2023-03-18 00:59:49,880] [INFO] Target genome list was writen to OceanDNA-b6789/target_genomes_gtdb.txt
[2023-03-18 00:59:49,921] [INFO] Task started: fastANI
[2023-03-18 00:59:49,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg762e0bfa-44ac-4b3b-b298-7ef261c63c31/OceanDNA-b6789.fa --refList OceanDNA-b6789/target_genomes_gtdb.txt --output OceanDNA-b6789/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:00:02,745] [INFO] Task succeeded: fastANI
[2023-03-18 01:00:02,758] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:00:02,758] [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	87.7164	543	737	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	79.1006	366	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000422685.1	s__Flavobacterium gelidilacus	78.9899	370	737	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	78.979	324	737	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	78.974	388	737	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	78.9492	391	737	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	78.944	335	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003293845.1	s__Flavobacterium tibetense	78.7268	316	737	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	78.6963	341	737	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	78.6431	293	737	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	78.6377	355	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_004363695.1	s__Flavobacterium cheniae	78.6355	357	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018401995.1	s__Flavobacterium sp018401995	78.6311	266	737	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	78.6292	337	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	78.5097	334	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002862755.1	s__Flavobacterium sp002862755	78.5067	325	737	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	78.4071	332	737	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	78.3768	350	737	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	78.3642	346	737	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	78.2844	344	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110615.1	s__Flavobacterium urocaniciphilum	78.0442	275	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019105125.1	s__Flavobacterium sp019105125	77.7265	177	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688495.1	s__Flavobacterium weaverense	77.4022	166	737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:00:02,760] [INFO] GTDB search result was written to OceanDNA-b6789/result_gtdb.tsv
[2023-03-18 01:00:02,760] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:00:02,763] [INFO] DFAST_QC result json was written to OceanDNA-b6789/dqc_result.json
[2023-03-18 01:00:02,764] [INFO] DFAST_QC completed!
[2023-03-18 01:00:02,764] [INFO] Total running time: 0h1m18s