[2023-03-18 02:27:37,198] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,199] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,199] [INFO] DQC Reference Directory: /var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference
[2023-03-18 02:27:38,462] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stg0b7c5625-966d-478d-b9e9-acc11d6c2f8e/OceanDNA-b10254.fa | prodigal -d OceanDNA-b10254/cds.fna -a OceanDNA-b10254/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:47,624] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:47,624] [INFO] Task started: HMMsearch
[2023-03-18 02:27:47,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b10254/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference/reference_markers.hmm OceanDNA-b10254/protein.faa > /dev/null
[2023-03-18 02:27:47,795] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:47,795] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b7c5625-966d-478d-b9e9-acc11d6c2f8e/OceanDNA-b10254.fa]
[2023-03-18 02:27:47,809] [INFO] Query marker FASTA was written to OceanDNA-b10254/markers.fasta
[2023-03-18 02:27:47,810] [INFO] Task started: Blastn
[2023-03-18 02:27:47,811] [INFO] Running command: blastn -query OceanDNA-b10254/markers.fasta -db /var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference/reference_markers.fasta -out OceanDNA-b10254/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:48,363] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:48,364] [INFO] Selected 21 target genomes.
[2023-03-18 02:27:48,364] [INFO] Target genome list was writen to OceanDNA-b10254/target_genomes.txt
[2023-03-18 02:27:48,372] [INFO] Task started: fastANI
[2023-03-18 02:27:48,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b7c5625-966d-478d-b9e9-acc11d6c2f8e/OceanDNA-b10254.fa --refList OceanDNA-b10254/target_genomes.txt --output OceanDNA-b10254/fastani_result.tsv --threads 1
[2023-03-18 02:27:59,755] [INFO] Task succeeded: fastANI
[2023-03-18 02:27:59,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:27:59,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:27:59,768] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:27:59,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:27:59,768] [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 porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	77.2008	144	451	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.2001	123	451	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	77.181	142	451	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	77.1534	149	451	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.1243	150	451	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	77.12	140	451	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	77.1165	141	451	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	77.0973	142	451	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.0859	153	451	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	77.0424	126	451	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.0263	126	451	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.0242	127	451	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.9743	143	451	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.9669	137	451	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.9663	146	451	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.9539	145	451	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.8846	133	451	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.8479	129	451	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.8468	137	451	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	76.7667	128	451	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	76.2668	74	451	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:27:59,768] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10254/tc_result.tsv
[2023-03-18 02:27:59,768] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:27:59,768] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:27:59,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference/checkm_data
[2023-03-18 02:27:59,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:27:59,772] [INFO] Task started: CheckM
[2023-03-18 02:27:59,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10254/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10254/checkm_input OceanDNA-b10254/checkm_result
[2023-03-18 02:28:27,702] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:27,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.87%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:27,705] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:27,705] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:27,705] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10254/markers.fasta)
[2023-03-18 02:28:27,705] [INFO] Task started: Blastn
[2023-03-18 02:28:27,705] [INFO] Running command: blastn -query OceanDNA-b10254/markers.fasta -db /var/lib/cwl/stg83cc59b8-02ed-442c-84a2-887b34ff42b5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10254/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:28,454] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:28,455] [INFO] Selected 12 target genomes.
[2023-03-18 02:28:28,455] [INFO] Target genome list was writen to OceanDNA-b10254/target_genomes_gtdb.txt
[2023-03-18 02:28:28,466] [INFO] Task started: fastANI
[2023-03-18 02:28:28,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b7c5625-966d-478d-b9e9-acc11d6c2f8e/OceanDNA-b10254.fa --refList OceanDNA-b10254/target_genomes_gtdb.txt --output OceanDNA-b10254/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:28:34,625] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:34,633] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:28:34,633] [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	99.1935	365	451	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	conclusive
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	83.6456	343	451	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_018608485.1	s__SCGC-AAA160-P02 sp018608485	82.7553	288	451	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	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	82.2943	346	451	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_905480405.1	s__Polaribacter sp905480405	77.2923	141	451	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	77.1611	168	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	76.9827	158	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152945.2	s__Polaribacter sp000152945	76.9551	125	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.8655	128	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	76.8468	137	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813915.1	s__Tenacibaculum sp002813915	76.6649	91	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	76.5183	130	451	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:28:34,634] [INFO] GTDB search result was written to OceanDNA-b10254/result_gtdb.tsv
[2023-03-18 02:28:34,634] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:28:34,636] [INFO] DFAST_QC result json was written to OceanDNA-b10254/dqc_result.json
[2023-03-18 02:28:34,636] [INFO] DFAST_QC completed!
[2023-03-18 02:28:34,636] [INFO] Total running time: 0h0m57s