[2024-01-25 19:30:36,650] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:30:36,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:30:36,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference
[2024-01-25 19:30:37,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:30:37,750] [INFO] Task started: Prodigal
[2024-01-25 19:30:37,750] [INFO] Running command: gunzip -c /var/lib/cwl/stgddf404e6-22d1-4fe3-9b47-9b677fff3e0c/GCF_014646035.1_ASM1464603v1_genomic.fna.gz | prodigal -d GCF_014646035.1_ASM1464603v1_genomic.fna/cds.fna -a GCF_014646035.1_ASM1464603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:30:47,586] [INFO] Task succeeded: Prodigal
[2024-01-25 19:30:47,587] [INFO] Task started: HMMsearch
[2024-01-25 19:30:47,587] [INFO] Running command: hmmsearch --tblout GCF_014646035.1_ASM1464603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference/reference_markers.hmm GCF_014646035.1_ASM1464603v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:30:47,795] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:30:47,796] [INFO] Found 6/6 markers.
[2024-01-25 19:30:47,832] [INFO] Query marker FASTA was written to GCF_014646035.1_ASM1464603v1_genomic.fna/markers.fasta
[2024-01-25 19:30:47,833] [INFO] Task started: Blastn
[2024-01-25 19:30:47,833] [INFO] Running command: blastn -query GCF_014646035.1_ASM1464603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference/reference_markers.fasta -out GCF_014646035.1_ASM1464603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:30:49,079] [INFO] Task succeeded: Blastn
[2024-01-25 19:30:49,083] [INFO] Selected 19 target genomes.
[2024-01-25 19:30:49,083] [INFO] Target genome list was writen to GCF_014646035.1_ASM1464603v1_genomic.fna/target_genomes.txt
[2024-01-25 19:30:49,091] [INFO] Task started: fastANI
[2024-01-25 19:30:49,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgddf404e6-22d1-4fe3-9b47-9b677fff3e0c/GCF_014646035.1_ASM1464603v1_genomic.fna.gz --refList GCF_014646035.1_ASM1464603v1_genomic.fna/target_genomes.txt --output GCF_014646035.1_ASM1464603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:31:09,276] [INFO] Task succeeded: fastANI
[2024-01-25 19:31:09,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:31:09,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:31:09,289] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:31:09,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:31:09,289] [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 deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	100.0	1394	1394	95	conclusive
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	99.9861	1378	1394	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	83.3809	896	1394	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.5214	824	1394	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	82.4415	934	1394	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	82.4323	922	1394	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.3447	857	1394	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.1397	861	1394	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.1183	859	1394	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.0345	761	1394	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	81.9231	850	1394	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.8941	785	1394	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	81.8193	829	1394	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	81.7366	867	1394	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.1862	749	1394	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.5325	647	1394	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.5324	680	1394	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.4109	664	1394	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.9999	702	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:31:09,291] [INFO] DFAST Taxonomy check result was written to GCF_014646035.1_ASM1464603v1_genomic.fna/tc_result.tsv
[2024-01-25 19:31:09,292] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:31:09,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:31:09,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference/checkm_data
[2024-01-25 19:31:09,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:31:09,332] [INFO] Task started: CheckM
[2024-01-25 19:31:09,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646035.1_ASM1464603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646035.1_ASM1464603v1_genomic.fna/checkm_input GCF_014646035.1_ASM1464603v1_genomic.fna/checkm_result
[2024-01-25 19:32:04,962] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:04,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:04,989] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:04,989] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:04,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646035.1_ASM1464603v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:04,990] [INFO] Task started: Blastn
[2024-01-25 19:32:04,990] [INFO] Running command: blastn -query GCF_014646035.1_ASM1464603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg477ed8d0-9a0d-44d9-b72f-340ca542a1c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646035.1_ASM1464603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:07,115] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:07,120] [INFO] Selected 15 target genomes.
[2024-01-25 19:32:07,120] [INFO] Target genome list was writen to GCF_014646035.1_ASM1464603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:07,128] [INFO] Task started: fastANI
[2024-01-25 19:32:07,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgddf404e6-22d1-4fe3-9b47-9b677fff3e0c/GCF_014646035.1_ASM1464603v1_genomic.fna.gz --refList GCF_014646035.1_ASM1464603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646035.1_ASM1464603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:23,507] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:23,516] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:23,517] [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_014266025.1	s__Nocardioides deserti	99.9861	1378	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_011250565.1	s__Nocardioides sp011250565	94.7897	1164	1394	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	88.3569	1095	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_014127485.1	s__Nocardioides sp014127485	83.4083	893	1394	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	82.5581	819	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_013155365.1	s__Nocardioides sp013155365	82.4066	859	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	82.3817	853	1394	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	82.1633	849	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002117935.1	s__Nocardioides sp002117935	82.0975	835	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.9952	765	1394	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	81.9058	852	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013466985.1	s__Nocardioides ungokensis	81.8974	785	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	81.7926	860	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_018275325.1	s__Nocardioides sp018275325	80.889	777	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	80.7148	703	1394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:23,518] [INFO] GTDB search result was written to GCF_014646035.1_ASM1464603v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:23,519] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:23,522] [INFO] DFAST_QC result json was written to GCF_014646035.1_ASM1464603v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:23,522] [INFO] DFAST_QC completed!
[2024-01-25 19:32:23,523] [INFO] Total running time: 0h1m47s