[2024-01-25 19:31:51,301] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,302] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,303] [INFO] DQC Reference Directory: /var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference
[2024-01-25 19:31:52,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,425] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg45073915-3afb-4095-b8e2-c5557f3c7e80/GCF_015070385.1_ASM1507038v1_genomic.fna.gz | prodigal -d GCF_015070385.1_ASM1507038v1_genomic.fna/cds.fna -a GCF_015070385.1_ASM1507038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:01,273] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:01,273] [INFO] Task started: HMMsearch
[2024-01-25 19:32:01,273] [INFO] Running command: hmmsearch --tblout GCF_015070385.1_ASM1507038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference/reference_markers.hmm GCF_015070385.1_ASM1507038v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:01,470] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:01,472] [INFO] Found 6/6 markers.
[2024-01-25 19:32:01,501] [INFO] Query marker FASTA was written to GCF_015070385.1_ASM1507038v1_genomic.fna/markers.fasta
[2024-01-25 19:32:01,501] [INFO] Task started: Blastn
[2024-01-25 19:32:01,502] [INFO] Running command: blastn -query GCF_015070385.1_ASM1507038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference/reference_markers.fasta -out GCF_015070385.1_ASM1507038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:02,702] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:02,705] [INFO] Selected 15 target genomes.
[2024-01-25 19:32:02,705] [INFO] Target genome list was writen to GCF_015070385.1_ASM1507038v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:02,709] [INFO] Task started: fastANI
[2024-01-25 19:32:02,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg45073915-3afb-4095-b8e2-c5557f3c7e80/GCF_015070385.1_ASM1507038v1_genomic.fna.gz --refList GCF_015070385.1_ASM1507038v1_genomic.fna/target_genomes.txt --output GCF_015070385.1_ASM1507038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:14,491] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:14,492] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:14,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:14,502] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:14,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:14,502] [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 malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	100.0	1051	1051	95	conclusive
Nocardioides daphniae	strain=JCM 16608	GCA_004777465.1	402297	402297	type	True	84.4606	770	1051	95	below_threshold
Nocardioides daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	84.4124	768	1051	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	83.5638	746	1051	95	below_threshold
Nocardioides gilvus	strain=XZ17	GCA_003194605.1	1735589	1735589	type	True	81.9124	666	1051	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	81.4339	639	1051	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	81.2672	547	1051	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	80.9162	583	1051	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.6229	554	1051	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.5837	548	1051	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.3737	565	1051	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	80.356	510	1051	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.284	568	1051	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.2472	531	1051	95	below_threshold
Nocardioides thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	79.7426	479	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:14,503] [INFO] DFAST Taxonomy check result was written to GCF_015070385.1_ASM1507038v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:14,504] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:14,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:14,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference/checkm_data
[2024-01-25 19:32:14,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:14,543] [INFO] Task started: CheckM
[2024-01-25 19:32:14,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015070385.1_ASM1507038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015070385.1_ASM1507038v1_genomic.fna/checkm_input GCF_015070385.1_ASM1507038v1_genomic.fna/checkm_result
[2024-01-25 19:33:12,444] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:12,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:12,463] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:12,463] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:12,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015070385.1_ASM1507038v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:12,464] [INFO] Task started: Blastn
[2024-01-25 19:33:12,464] [INFO] Running command: blastn -query GCF_015070385.1_ASM1507038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc273a7d4-6371-41b3-9843-ce67daf20b36/dqc_reference/reference_markers_gtdb.fasta -out GCF_015070385.1_ASM1507038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:14,403] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:14,406] [INFO] Selected 20 target genomes.
[2024-01-25 19:33:14,406] [INFO] Target genome list was writen to GCF_015070385.1_ASM1507038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:14,416] [INFO] Task started: fastANI
[2024-01-25 19:33:14,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg45073915-3afb-4095-b8e2-c5557f3c7e80/GCF_015070385.1_ASM1507038v1_genomic.fna.gz --refList GCF_015070385.1_ASM1507038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015070385.1_ASM1507038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:33:30,486] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:30,499] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:33:30,499] [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_004777465.1	s__Nocardioides daphniae	84.438	772	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.94	99.94	1.00	1.00	2	-
GCF_006007965.1	s__Nocardioides sp006007965	83.5633	746	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194605.1	s__Nocardioides gilvus	81.9125	666	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	81.391	643	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014875.1	s__Nocardioides sp004014875	81.2919	545	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013624435.2	s__Nocardioides sp013624415	81.21	636	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_002865585.1	s__Nocardioides houyundeii	80.9155	583	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_013155365.1	s__Nocardioides sp013155365	80.6084	537	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	80.5397	448	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011420305.2	s__Nocardioides sp011420305	80.4863	538	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_001429625.1	s__Nocardioides sp001429625	80.3908	564	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	80.3786	564	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	80.3773	543	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408145.1	s__Nocardioides marinus	80.3707	508	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_004137255.1	s__Nocardioides oleivorans	80.2945	549	1051	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	80.2278	538	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003057875.1	s__Nocardioides currus	80.0999	557	1051	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	79.9914	483	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522105.1	s__Nocardioides sp004522105	79.8028	540	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410655.1	s__Nocardioides thalensis	79.7107	482	1051	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:33:30,502] [INFO] GTDB search result was written to GCF_015070385.1_ASM1507038v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:33:30,504] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:33:30,508] [INFO] DFAST_QC result json was written to GCF_015070385.1_ASM1507038v1_genomic.fna/dqc_result.json
[2024-01-25 19:33:30,508] [INFO] DFAST_QC completed!
[2024-01-25 19:33:30,508] [INFO] Total running time: 0h1m39s