[2023-03-18 03:45:10,234] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference
[2023-03-18 03:45:11,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:11,974] [INFO] Task started: Prodigal
[2023-03-18 03:45:11,974] [INFO] Running command: cat /var/lib/cwl/stgdc362eae-7e8f-44ae-8ec7-de0a812a2c88/OceanDNA-b3329.fa | prodigal -d OceanDNA-b3329/cds.fna -a OceanDNA-b3329/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:18,490] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:18,490] [INFO] Task started: HMMsearch
[2023-03-18 03:45:18,490] [INFO] Running command: hmmsearch --tblout OceanDNA-b3329/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference/reference_markers.hmm OceanDNA-b3329/protein.faa > /dev/null
[2023-03-18 03:45:18,635] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:18,636] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdc362eae-7e8f-44ae-8ec7-de0a812a2c88/OceanDNA-b3329.fa]
[2023-03-18 03:45:18,653] [INFO] Query marker FASTA was written to OceanDNA-b3329/markers.fasta
[2023-03-18 03:45:18,653] [INFO] Task started: Blastn
[2023-03-18 03:45:18,653] [INFO] Running command: blastn -query OceanDNA-b3329/markers.fasta -db /var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference/reference_markers.fasta -out OceanDNA-b3329/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:20,205] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:20,206] [INFO] Selected 20 target genomes.
[2023-03-18 03:45:20,206] [INFO] Target genome list was writen to OceanDNA-b3329/target_genomes.txt
[2023-03-18 03:45:20,216] [INFO] Task started: fastANI
[2023-03-18 03:45:20,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc362eae-7e8f-44ae-8ec7-de0a812a2c88/OceanDNA-b3329.fa --refList OceanDNA-b3329/target_genomes.txt --output OceanDNA-b3329/fastani_result.tsv --threads 1
[2023-03-18 03:45:31,183] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:31,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:31,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:31,195] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:31,195] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:31,195] [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	92.8258	105	111	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	84.6431	94	111	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	84.6168	90	111	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	84.6168	90	111	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	84.6039	93	111	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	84.016	82	111	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	83.9055	83	111	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	83.6577	77	111	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	83.4028	85	111	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	83.4001	79	111	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	82.8296	73	111	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.4707	71	111	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	82.4547	75	111	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	82.2553	67	111	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	82.1855	68	111	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	82.0549	69	111	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	81.7356	65	111	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.6662	77	111	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	81.2064	64	111	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.1381	76	111	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:31,196] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3329/tc_result.tsv
[2023-03-18 03:45:31,196] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:31,196] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:31,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference/checkm_data
[2023-03-18 03:45:31,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:31,200] [INFO] Task started: CheckM
[2023-03-18 03:45:31,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3329/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3329/checkm_input OceanDNA-b3329/checkm_result
[2023-03-18 03:45:52,796] [INFO] Task succeeded: CheckM
[2023-03-18 03:45:52,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.38%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:45:52,799] [INFO] ===== Completeness check finished =====
[2023-03-18 03:45:52,799] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:45:52,799] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3329/markers.fasta)
[2023-03-18 03:45:52,799] [INFO] Task started: Blastn
[2023-03-18 03:45:52,799] [INFO] Running command: blastn -query OceanDNA-b3329/markers.fasta -db /var/lib/cwl/stg848e960c-88d0-4246-a120-ba26b7d4e98f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3329/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:54,169] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:54,170] [INFO] Selected 13 target genomes.
[2023-03-18 03:45:54,170] [INFO] Target genome list was writen to OceanDNA-b3329/target_genomes_gtdb.txt
[2023-03-18 03:45:54,228] [INFO] Task started: fastANI
[2023-03-18 03:45:54,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc362eae-7e8f-44ae-8ec7-de0a812a2c88/OceanDNA-b3329.fa --refList OceanDNA-b3329/target_genomes_gtdb.txt --output OceanDNA-b3329/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:01,918] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:01,926] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:46:01,926] [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
GCF_013408145.1	s__Nocardioides marinus	92.8258	105	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_001627335.1	s__Nocardioides sp001627335	91.9673	93	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCA_009701885.1	s__Nocardioides sp009701885	87.8714	91	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653335.1	s__Nocardioides dokdonensis	84.5878	79	111	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	84.5086	91	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013466785.1	s__Nocardioides marinisabuli	84.4949	94	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	84.3741	80	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_011250565.1	s__Nocardioides sp011250565	84.0788	81	111	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	83.6577	77	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	83.4028	85	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_009823805.1	s__Nocardioides sp009823805	82.4547	75	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047265.1	s__Nocardioides terrigena	82.1855	68	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_013466985.1	s__Nocardioides ungokensis	81.6662	77	111	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:01,926] [INFO] GTDB search result was written to OceanDNA-b3329/result_gtdb.tsv
[2023-03-18 03:46:01,926] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:01,928] [INFO] DFAST_QC result json was written to OceanDNA-b3329/dqc_result.json
[2023-03-18 03:46:01,928] [INFO] DFAST_QC completed!
[2023-03-18 03:46:01,928] [INFO] Total running time: 0h0m52s