[2023-03-15 14:47:21,433] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference
[2023-03-15 14:47:22,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,552] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,552] [INFO] Running command: cat /var/lib/cwl/stg8b978835-cfc2-4095-9cbe-5aa21dc77b36/OceanDNA-b10236.fa | prodigal -d OceanDNA-b10236/cds.fna -a OceanDNA-b10236/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:30,351] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:30,351] [INFO] Task started: HMMsearch
[2023-03-15 14:47:30,352] [INFO] Running command: hmmsearch --tblout OceanDNA-b10236/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference/reference_markers.hmm OceanDNA-b10236/protein.faa > /dev/null
[2023-03-15 14:47:30,502] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:30,502] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8b978835-cfc2-4095-9cbe-5aa21dc77b36/OceanDNA-b10236.fa]
[2023-03-15 14:47:30,518] [INFO] Query marker FASTA was written to OceanDNA-b10236/markers.fasta
[2023-03-15 14:47:30,518] [INFO] Task started: Blastn
[2023-03-15 14:47:30,518] [INFO] Running command: blastn -query OceanDNA-b10236/markers.fasta -db /var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference/reference_markers.fasta -out OceanDNA-b10236/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:31,033] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:31,035] [INFO] Selected 17 target genomes.
[2023-03-15 14:47:31,036] [INFO] Target genome list was writen to OceanDNA-b10236/target_genomes.txt
[2023-03-15 14:47:31,045] [INFO] Task started: fastANI
[2023-03-15 14:47:31,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b978835-cfc2-4095-9cbe-5aa21dc77b36/OceanDNA-b10236.fa --refList OceanDNA-b10236/target_genomes.txt --output OceanDNA-b10236/fastani_result.tsv --threads 1
[2023-03-15 14:47:39,797] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:39,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:47:39,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:47:39,807] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:47:39,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:47:39,808] [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
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	77.1131	143	404	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.0954	144	404	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.0749	113	404	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.931	125	404	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.9257	139	404	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.9064	124	404	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.8514	144	404	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.8069	147	404	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.7793	114	404	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.7316	126	404	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.7102	111	404	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.6147	111	404	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	76.595	130	404	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	76.5884	126	404	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.5725	128	404	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	76.5234	130	404	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.4179	104	404	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:47:39,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10236/tc_result.tsv
[2023-03-15 14:47:39,811] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:47:39,811] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:47:39,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference/checkm_data
[2023-03-15 14:47:39,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:47:39,816] [INFO] Task started: CheckM
[2023-03-15 14:47:39,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10236/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10236/checkm_input OceanDNA-b10236/checkm_result
[2023-03-15 14:48:04,626] [INFO] Task succeeded: CheckM
[2023-03-15 14:48:04,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:48:04,645] [INFO] ===== Completeness check finished =====
[2023-03-15 14:48:04,645] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:48:04,645] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10236/markers.fasta)
[2023-03-15 14:48:04,645] [INFO] Task started: Blastn
[2023-03-15 14:48:04,646] [INFO] Running command: blastn -query OceanDNA-b10236/markers.fasta -db /var/lib/cwl/stgeb8ad0a9-cd97-48e9-b985-02f3d5d3a9e2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10236/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:48:05,299] [INFO] Task succeeded: Blastn
[2023-03-15 14:48:05,304] [INFO] Selected 13 target genomes.
[2023-03-15 14:48:05,304] [INFO] Target genome list was writen to OceanDNA-b10236/target_genomes_gtdb.txt
[2023-03-15 14:48:05,353] [INFO] Task started: fastANI
[2023-03-15 14:48:05,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b978835-cfc2-4095-9cbe-5aa21dc77b36/OceanDNA-b10236.fa --refList OceanDNA-b10236/target_genomes_gtdb.txt --output OceanDNA-b10236/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:48:11,725] [INFO] Task succeeded: fastANI
[2023-03-15 14:48:11,734] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:48:11,734] [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_905479435.1	s__SCGC-AAA160-P02 sp905479435	88.8442	302	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	82.8404	301	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	82.2253	306	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCA_018608485.1	s__SCGC-AAA160-P02 sp018608485	81.9267	262	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	-
GCF_002163835.1	s__Polaribacter sp002163835	77.1595	127	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	77.135	150	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763215.1	s__SCGC-AAA160-P02 sp016763215	76.9448	81	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	76.9257	139	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	76.9064	124	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007827455.1	s__VISM01 sp007827455	76.8414	133	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	76.826	127	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	76.8029	101	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	76.5441	138	404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:48:11,735] [INFO] GTDB search result was written to OceanDNA-b10236/result_gtdb.tsv
[2023-03-15 14:48:11,739] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:48:11,742] [INFO] DFAST_QC result json was written to OceanDNA-b10236/dqc_result.json
[2023-03-15 14:48:11,742] [INFO] DFAST_QC completed!
[2023-03-15 14:48:11,742] [INFO] Total running time: 0h0m50s