[2023-03-18 08:55:50,589] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,589] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference
[2023-03-18 08:55:51,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,802] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,802] [INFO] Running command: cat /var/lib/cwl/stg219d4327-63ed-4f8f-95cb-c5f763e70adb/OceanDNA-b3318.fa | prodigal -d OceanDNA-b3318/cds.fna -a OceanDNA-b3318/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:19,824] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:19,824] [INFO] Task started: HMMsearch
[2023-03-18 08:56:19,824] [INFO] Running command: hmmsearch --tblout OceanDNA-b3318/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference/reference_markers.hmm OceanDNA-b3318/protein.faa > /dev/null
[2023-03-18 08:56:20,122] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:20,122] [INFO] Found 6/6 markers.
[2023-03-18 08:56:20,153] [INFO] Query marker FASTA was written to OceanDNA-b3318/markers.fasta
[2023-03-18 08:56:20,157] [INFO] Task started: Blastn
[2023-03-18 08:56:20,157] [INFO] Running command: blastn -query OceanDNA-b3318/markers.fasta -db /var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference/reference_markers.fasta -out OceanDNA-b3318/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:21,267] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:21,269] [INFO] Selected 24 target genomes.
[2023-03-18 08:56:21,269] [INFO] Target genome list was writen to OceanDNA-b3318/target_genomes.txt
[2023-03-18 08:56:21,285] [INFO] Task started: fastANI
[2023-03-18 08:56:21,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg219d4327-63ed-4f8f-95cb-c5f763e70adb/OceanDNA-b3318.fa --refList OceanDNA-b3318/target_genomes.txt --output OceanDNA-b3318/fastani_result.tsv --threads 1
[2023-03-18 08:56:43,900] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:43,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:43,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:43,914] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:43,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:43,914] [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
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	82.0215	924	1530	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	81.5308	833	1530	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	81.314	776	1530	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.2538	779	1530	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.2031	789	1530	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	81.1874	792	1530	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.1273	777	1530	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.119	766	1530	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	81.0949	795	1530	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	81.0812	806	1530	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.9764	757	1530	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.9606	748	1530	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.9099	743	1530	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.7712	737	1530	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.7621	727	1530	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.7258	821	1530	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.6591	830	1530	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	80.3539	727	1530	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.9668	640	1530	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.8506	637	1530	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.8419	658	1530	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.8003	645	1530	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.7592	721	1530	95	below_threshold
Marmoricola ginsengisoli	strain=Gsoil 097	GCA_003725695.1	661483	661483	type	True	79.3426	556	1530	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:43,915] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3318/tc_result.tsv
[2023-03-18 08:56:43,915] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:43,915] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:43,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference/checkm_data
[2023-03-18 08:56:43,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:43,929] [INFO] Task started: CheckM
[2023-03-18 08:56:43,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3318/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3318/checkm_input OceanDNA-b3318/checkm_result
[2023-03-18 08:58:17,018] [INFO] Task succeeded: CheckM
[2023-03-18 08:58:17,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:58:17,034] [INFO] ===== Completeness check finished =====
[2023-03-18 08:58:17,035] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:58:17,035] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3318/markers.fasta)
[2023-03-18 08:58:17,037] [INFO] Task started: Blastn
[2023-03-18 08:58:17,037] [INFO] Running command: blastn -query OceanDNA-b3318/markers.fasta -db /var/lib/cwl/stg807fef63-a8d7-4072-8035-441c0e0f6c71/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3318/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:58:18,903] [INFO] Task succeeded: Blastn
[2023-03-18 08:58:18,904] [INFO] Selected 18 target genomes.
[2023-03-18 08:58:18,904] [INFO] Target genome list was writen to OceanDNA-b3318/target_genomes_gtdb.txt
[2023-03-18 08:58:18,918] [INFO] Task started: fastANI
[2023-03-18 08:58:18,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg219d4327-63ed-4f8f-95cb-c5f763e70adb/OceanDNA-b3318.fa --refList OceanDNA-b3318/target_genomes_gtdb.txt --output OceanDNA-b3318/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:58:36,224] [INFO] Task succeeded: fastANI
[2023-03-18 08:58:36,235] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:58:36,235] [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_002698575.1	s__Nocardioides sp002698575	90.8244	1083	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087085.1	s__Nocardioides rubriscoriae	82.0658	918	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	81.8701	827	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_004522105.1	s__Nocardioides sp004522105	81.6677	844	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346315.1	s__Nocardioides litoris	81.5299	833	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	81.2774	780	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015024225.1	s__Nocardioides sp015024225	81.1607	795	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.1518	763	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	81.0974	794	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004522095.1	s__Nocardioides sp004522095	81.095	812	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	80.9292	752	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_014127485.1	s__Nocardioides sp014127485	80.8898	745	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCA_009702305.1	s__Nocardioides sp009702305	80.8745	475	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	80.7162	719	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011420305.2	s__Nocardioides sp011420305	80.5868	667	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.516	794	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013155365.1	s__Nocardioides sp013155365	80.508	686	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	79.9643	713	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:58:36,236] [INFO] GTDB search result was written to OceanDNA-b3318/result_gtdb.tsv
[2023-03-18 08:58:36,236] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:58:36,239] [INFO] DFAST_QC result json was written to OceanDNA-b3318/dqc_result.json
[2023-03-18 08:58:36,239] [INFO] DFAST_QC completed!
[2023-03-18 08:58:36,239] [INFO] Total running time: 0h2m46s