[2023-03-15 12:13:55,704] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:13:55,706] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:13:55,707] [INFO] DQC Reference Directory: /var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference
[2023-03-15 12:13:57,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:13:57,410] [INFO] Task started: Prodigal
[2023-03-15 12:13:57,410] [INFO] Running command: cat /var/lib/cwl/stga9319013-d099-4548-949e-496442235505/OceanDNA-b3323.fa | prodigal -d OceanDNA-b3323/cds.fna -a OceanDNA-b3323/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:14:13,025] [INFO] Task succeeded: Prodigal
[2023-03-15 12:14:13,025] [INFO] Task started: HMMsearch
[2023-03-15 12:14:13,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b3323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference/reference_markers.hmm OceanDNA-b3323/protein.faa > /dev/null
[2023-03-15 12:14:13,233] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:14:13,234] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga9319013-d099-4548-949e-496442235505/OceanDNA-b3323.fa]
[2023-03-15 12:14:13,290] [INFO] Query marker FASTA was written to OceanDNA-b3323/markers.fasta
[2023-03-15 12:14:13,292] [INFO] Task started: Blastn
[2023-03-15 12:14:13,292] [INFO] Running command: blastn -query OceanDNA-b3323/markers.fasta -db /var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference/reference_markers.fasta -out OceanDNA-b3323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:14:14,269] [INFO] Task succeeded: Blastn
[2023-03-15 12:14:14,284] [INFO] Selected 24 target genomes.
[2023-03-15 12:14:14,285] [INFO] Target genome list was writen to OceanDNA-b3323/target_genomes.txt
[2023-03-15 12:14:14,301] [INFO] Task started: fastANI
[2023-03-15 12:14:14,301] [INFO] Running command: fastANI --query /var/lib/cwl/stga9319013-d099-4548-949e-496442235505/OceanDNA-b3323.fa --refList OceanDNA-b3323/target_genomes.txt --output OceanDNA-b3323/fastani_result.tsv --threads 1
[2023-03-15 12:14:34,086] [INFO] Task succeeded: fastANI
[2023-03-15 12:14:34,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:14:34,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:14:34,100] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:14:34,100] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:14:34,100] [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	90.4452	746	831	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	83.3028	604	831	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	83.2944	605	831	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	82.9779	579	831	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.8913	598	831	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.8718	599	831	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.3965	543	831	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.3593	542	831	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.1187	466	831	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.7855	481	831	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	80.6903	484	831	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.6185	488	831	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	80.6075	461	831	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	80.4543	491	831	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.4319	466	831	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.3704	459	831	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.3183	448	831	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.1735	434	831	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	80.0401	436	831	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.9905	412	831	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.9284	445	831	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.8992	477	831	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.8066	420	831	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.7025	438	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:14:34,109] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3323/tc_result.tsv
[2023-03-15 12:14:34,124] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:14:34,124] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:14:34,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference/checkm_data
[2023-03-15 12:14:34,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:14:34,146] [INFO] Task started: CheckM
[2023-03-15 12:14:34,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3323/checkm_input OceanDNA-b3323/checkm_result
[2023-03-15 12:15:15,319] [INFO] Task succeeded: CheckM
[2023-03-15 12:15:15,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.55%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 12:15:15,410] [INFO] ===== Completeness check finished =====
[2023-03-15 12:15:15,410] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:15:15,410] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3323/markers.fasta)
[2023-03-15 12:15:15,411] [INFO] Task started: Blastn
[2023-03-15 12:15:15,411] [INFO] Running command: blastn -query OceanDNA-b3323/markers.fasta -db /var/lib/cwl/stgd32b1894-a985-4c11-ae24-6b73aa917540/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:15:17,006] [INFO] Task succeeded: Blastn
[2023-03-15 12:15:17,011] [INFO] Selected 18 target genomes.
[2023-03-15 12:15:17,011] [INFO] Target genome list was writen to OceanDNA-b3323/target_genomes_gtdb.txt
[2023-03-15 12:15:17,196] [INFO] Task started: fastANI
[2023-03-15 12:15:17,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga9319013-d099-4548-949e-496442235505/OceanDNA-b3323.fa --refList OceanDNA-b3323/target_genomes_gtdb.txt --output OceanDNA-b3323/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:15:32,093] [INFO] Task succeeded: fastANI
[2023-03-15 12:15:32,104] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:15:32,104] [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	93.4363	678	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_013408145.1	s__Nocardioides marinus	90.4452	746	831	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	85.9046	651	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466785.1	s__Nocardioides marinisabuli	83.3347	602	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907435.1	s__Nocardioides salarius	82.9094	584	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001653335.1	s__Nocardioides dokdonensis	82.1543	572	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	81.7627	523	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	81.6055	527	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_014266025.1	s__Nocardioides deserti	81.4362	536	831	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	81.3253	527	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_015319165.1	s__Nocardioides acrostichi	81.2624	511	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.0953	468	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	81.085	511	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	80.9745	499	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003047265.1	s__Nocardioides terrigena	80.5888	462	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_004137345.1	s__Nocardioides sp004137345	80.0265	438	831	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	79.8494	491	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213595.1	s__Fen-668 sp016213595	77.0141	91	831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:15:32,117] [INFO] GTDB search result was written to OceanDNA-b3323/result_gtdb.tsv
[2023-03-15 12:15:32,139] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:15:32,152] [INFO] DFAST_QC result json was written to OceanDNA-b3323/dqc_result.json
[2023-03-15 12:15:32,152] [INFO] DFAST_QC completed!
[2023-03-15 12:15:32,152] [INFO] Total running time: 0h1m36s