[2024-01-24 13:57:43,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference
[2024-01-24 13:57:45,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,107] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,107] [INFO] Running command: gunzip -c /var/lib/cwl/stgae3e1ff4-efa7-4af0-84fa-ac3fd9982d3d/GCF_013408145.1_ASM1340814v1_genomic.fna.gz | prodigal -d GCF_013408145.1_ASM1340814v1_genomic.fna/cds.fna -a GCF_013408145.1_ASM1340814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,839] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,840] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,840] [INFO] Running command: hmmsearch --tblout GCF_013408145.1_ASM1340814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference/reference_markers.hmm GCF_013408145.1_ASM1340814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,130] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,132] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,181] [INFO] Query marker FASTA was written to GCF_013408145.1_ASM1340814v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,182] [INFO] Task started: Blastn
[2024-01-24 13:57:57,182] [INFO] Running command: blastn -query GCF_013408145.1_ASM1340814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference/reference_markers.fasta -out GCF_013408145.1_ASM1340814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,556] [INFO] Selected 21 target genomes.
[2024-01-24 13:57:58,557] [INFO] Target genome list was writen to GCF_013408145.1_ASM1340814v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,566] [INFO] Task started: fastANI
[2024-01-24 13:57:58,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3e1ff4-efa7-4af0-84fa-ac3fd9982d3d/GCF_013408145.1_ASM1340814v1_genomic.fna.gz --refList GCF_013408145.1_ASM1340814v1_genomic.fna/target_genomes.txt --output GCF_013408145.1_ASM1340814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:20,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:20,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:20,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:20,507] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:20,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:20,507] [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	100.0	1370	1370	95	conclusive
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	83.4771	905	1370	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	83.4357	906	1370	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	83.3865	917	1370	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	83.3367	907	1370	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	83.3324	904	1370	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.1987	829	1370	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.9597	796	1370	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.8633	827	1370	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.8392	819	1370	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.7206	823	1370	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.5394	735	1370	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.3375	749	1370	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	81.3029	724	1370	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.8913	720	1370	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.7959	670	1370	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.7176	702	1370	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.4923	636	1370	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.3563	640	1370	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.2748	679	1370	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.251	649	1370	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:20,509] [INFO] DFAST Taxonomy check result was written to GCF_013408145.1_ASM1340814v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:20,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:20,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:20,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference/checkm_data
[2024-01-24 13:58:20,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:20,558] [INFO] Task started: CheckM
[2024-01-24 13:58:20,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408145.1_ASM1340814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408145.1_ASM1340814v1_genomic.fna/checkm_input GCF_013408145.1_ASM1340814v1_genomic.fna/checkm_result
[2024-01-24 13:59:34,472] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:34,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:34,494] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:34,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:34,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408145.1_ASM1340814v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:34,495] [INFO] Task started: Blastn
[2024-01-24 13:59:34,495] [INFO] Running command: blastn -query GCF_013408145.1_ASM1340814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4611ae6b-36d3-4e84-8efd-cfcde7a2401b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408145.1_ASM1340814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:36,565] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:36,570] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:36,570] [INFO] Target genome list was writen to GCF_013408145.1_ASM1340814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:36,773] [INFO] Task started: fastANI
[2024-01-24 13:59:36,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgae3e1ff4-efa7-4af0-84fa-ac3fd9982d3d/GCF_013408145.1_ASM1340814v1_genomic.fna.gz --refList GCF_013408145.1_ASM1340814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408145.1_ASM1340814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:55,064] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:55,080] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:55,080] [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	100.0	1369	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	conclusive
GCA_001627335.1	s__Nocardioides sp001627335	90.4561	1010	1370	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	86.3644	1025	1370	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	83.5035	898	1370	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	83.3467	917	1370	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	82.866	886	1370	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	82.2198	827	1370	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	82.1498	820	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	81.9248	800	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014266025.1	s__Nocardioides deserti	81.7975	822	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009557055.1	s__Nocardioides sp009557055	81.7092	737	1370	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	81.656	753	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.4669	737	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	81.3252	750	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	80.9664	758	1370	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	80.531	705	1370	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:55,082] [INFO] GTDB search result was written to GCF_013408145.1_ASM1340814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:55,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:55,088] [INFO] DFAST_QC result json was written to GCF_013408145.1_ASM1340814v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:55,088] [INFO] DFAST_QC completed!
[2024-01-24 13:59:55,089] [INFO] Total running time: 0h2m11s