[2023-03-17 23:02:14,734] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:02:14,734] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:02:14,734] [INFO] DQC Reference Directory: /var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference
[2023-03-17 23:02:15,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:02:15,845] [INFO] Task started: Prodigal
[2023-03-17 23:02:15,845] [INFO] Running command: cat /var/lib/cwl/stg123a39c3-a41d-4d9a-a999-b47115b47060/OceanDNA-b3372.fa | prodigal -d OceanDNA-b3372/cds.fna -a OceanDNA-b3372/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:02:38,048] [INFO] Task succeeded: Prodigal
[2023-03-17 23:02:38,049] [INFO] Task started: HMMsearch
[2023-03-17 23:02:38,049] [INFO] Running command: hmmsearch --tblout OceanDNA-b3372/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference/reference_markers.hmm OceanDNA-b3372/protein.faa > /dev/null
[2023-03-17 23:02:38,248] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:02:38,249] [INFO] Found 6/6 markers.
[2023-03-17 23:02:38,271] [INFO] Query marker FASTA was written to OceanDNA-b3372/markers.fasta
[2023-03-17 23:02:38,272] [INFO] Task started: Blastn
[2023-03-17 23:02:38,273] [INFO] Running command: blastn -query OceanDNA-b3372/markers.fasta -db /var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference/reference_markers.fasta -out OceanDNA-b3372/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:02:39,453] [INFO] Task succeeded: Blastn
[2023-03-17 23:02:39,454] [INFO] Selected 22 target genomes.
[2023-03-17 23:02:39,454] [INFO] Target genome list was writen to OceanDNA-b3372/target_genomes.txt
[2023-03-17 23:02:39,466] [INFO] Task started: fastANI
[2023-03-17 23:02:39,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg123a39c3-a41d-4d9a-a999-b47115b47060/OceanDNA-b3372.fa --refList OceanDNA-b3372/target_genomes.txt --output OceanDNA-b3372/fastani_result.tsv --threads 1
[2023-03-17 23:03:02,086] [INFO] Task succeeded: fastANI
[2023-03-17 23:03:02,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:03:02,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:03:02,099] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:03:02,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:03:02,099] [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 marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	90.5999	1087	1228	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	83.3957	858	1228	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	83.372	859	1228	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	83.3651	863	1228	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.445	799	1228	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.1383	777	1228	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.0958	784	1228	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.9772	772	1228	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.6649	798	1228	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.6373	767	1228	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.5667	704	1228	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	81.4437	710	1228	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.4374	710	1228	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.3258	708	1228	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	81.2299	652	1228	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	81.0749	644	1228	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.9887	694	1228	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.8735	670	1228	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.5789	590	1228	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.5589	699	1228	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.3607	646	1228	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.3349	655	1228	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:03:02,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3372/tc_result.tsv
[2023-03-17 23:03:02,100] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:03:02,100] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:03:02,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference/checkm_data
[2023-03-17 23:03:02,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:03:02,106] [INFO] Task started: CheckM
[2023-03-17 23:03:02,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3372/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3372/checkm_input OceanDNA-b3372/checkm_result
[2023-03-17 23:04:18,178] [INFO] Task succeeded: CheckM
[2023-03-17 23:04:18,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:04:18,187] [INFO] ===== Completeness check finished =====
[2023-03-17 23:04:18,187] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:04:18,187] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3372/markers.fasta)
[2023-03-17 23:04:18,188] [INFO] Task started: Blastn
[2023-03-17 23:04:18,188] [INFO] Running command: blastn -query OceanDNA-b3372/markers.fasta -db /var/lib/cwl/stg581220c5-4eba-4bd3-a1fd-71c6a9c55a72/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3372/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:04:20,273] [INFO] Task succeeded: Blastn
[2023-03-17 23:04:20,277] [INFO] Selected 16 target genomes.
[2023-03-17 23:04:20,277] [INFO] Target genome list was writen to OceanDNA-b3372/target_genomes_gtdb.txt
[2023-03-17 23:04:20,291] [INFO] Task started: fastANI
[2023-03-17 23:04:20,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg123a39c3-a41d-4d9a-a999-b47115b47060/OceanDNA-b3372.fa --refList OceanDNA-b3372/target_genomes_gtdb.txt --output OceanDNA-b3372/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:04:35,686] [INFO] Task succeeded: fastANI
[2023-03-17 23:04:35,695] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:04:35,696] [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_001627335.1	s__Nocardioides sp001627335	99.9428	1094	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	conclusive
GCF_013408145.1	s__Nocardioides marinus	90.6035	1086	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_009701885.1	s__Nocardioides sp009701885	86.4425	971	1228	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	83.3939	860	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015070375.1	s__Nocardioides kribbensis	82.4652	797	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_011250565.1	s__Nocardioides sp011250565	82.3701	765	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	82.127	777	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014127485.1	s__Nocardioides sp014127485	82.1141	755	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	82.0159	768	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.6708	797	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009702305.1	s__Nocardioides sp009702305	81.6337	494	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	81.4523	709	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	80.892	667	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	80.846	662	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919105.1	s__Nocardioides sp004919105	80.7188	679	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	80.5051	719	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:04:35,697] [INFO] GTDB search result was written to OceanDNA-b3372/result_gtdb.tsv
[2023-03-17 23:04:35,699] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:04:35,703] [INFO] DFAST_QC result json was written to OceanDNA-b3372/dqc_result.json
[2023-03-17 23:04:35,703] [INFO] DFAST_QC completed!
[2023-03-17 23:04:35,703] [INFO] Total running time: 0h2m21s