[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg34ec1f74-8bb6-4d0b-b739-8ebc2664ba48/GCF_014127485.1_ASM1412748v1_genomic.fna.gz | prodigal -d GCF_014127485.1_ASM1412748v1_genomic.fna/cds.fna -a GCF_014127485.1_ASM1412748v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,473] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,473] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,474] [INFO] Running command: hmmsearch --tblout GCF_014127485.1_ASM1412748v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference/reference_markers.hmm GCF_014127485.1_ASM1412748v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,731] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,736] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,772] [INFO] Query marker FASTA was written to GCF_014127485.1_ASM1412748v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,772] [INFO] Task started: Blastn
[2024-01-24 10:47:23,772] [INFO] Running command: blastn -query GCF_014127485.1_ASM1412748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference/reference_markers.fasta -out GCF_014127485.1_ASM1412748v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,113] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,117] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:25,118] [INFO] Target genome list was writen to GCF_014127485.1_ASM1412748v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,189] [INFO] Task started: fastANI
[2024-01-24 10:47:25,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg34ec1f74-8bb6-4d0b-b739-8ebc2664ba48/GCF_014127485.1_ASM1412748v1_genomic.fna.gz --refList GCF_014127485.1_ASM1412748v1_genomic.fna/target_genomes.txt --output GCF_014127485.1_ASM1412748v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:49,421] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:49,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:49,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:49,439] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:49,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:49,440] [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 dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	100.0	1402	1402	95	conclusive
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	84.6367	1004	1402	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	84.619	1029	1402	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	83.4132	913	1402	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	83.3714	914	1402	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	82.7665	873	1402	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.7599	815	1402	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	82.5965	841	1402	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	82.5834	839	1402	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	82.5585	854	1402	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.4999	796	1402	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	82.4667	850	1402	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.3906	861	1402	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.3663	864	1402	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.3485	812	1402	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	82.2558	801	1402	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.8681	811	1402	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.2387	769	1402	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.6282	754	1402	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	80.6215	662	1402	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.3086	672	1402	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.2788	711	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:49,442] [INFO] DFAST Taxonomy check result was written to GCF_014127485.1_ASM1412748v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:49,444] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:49,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:49,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference/checkm_data
[2024-01-24 10:47:49,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:49,503] [INFO] Task started: CheckM
[2024-01-24 10:47:49,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014127485.1_ASM1412748v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014127485.1_ASM1412748v1_genomic.fna/checkm_input GCF_014127485.1_ASM1412748v1_genomic.fna/checkm_result
[2024-01-24 10:48:50,206] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:50,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:50,224] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:50,224] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:50,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014127485.1_ASM1412748v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:50,225] [INFO] Task started: Blastn
[2024-01-24 10:48:50,225] [INFO] Running command: blastn -query GCF_014127485.1_ASM1412748v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c97d8b8-404e-4c6e-8279-497a46962596/dqc_reference/reference_markers_gtdb.fasta -out GCF_014127485.1_ASM1412748v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:52,200] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:52,203] [INFO] Selected 18 target genomes.
[2024-01-24 10:48:52,203] [INFO] Target genome list was writen to GCF_014127485.1_ASM1412748v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:52,216] [INFO] Task started: fastANI
[2024-01-24 10:48:52,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg34ec1f74-8bb6-4d0b-b739-8ebc2664ba48/GCF_014127485.1_ASM1412748v1_genomic.fna.gz --refList GCF_014127485.1_ASM1412748v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014127485.1_ASM1412748v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:12,357] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:12,371] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:12,372] [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_014127485.1	s__Nocardioides sp014127485	100.0	1402	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	conclusive
GCF_900101465.1	s__Nocardioides lianchengensis	84.6616	1001	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013177455.1	s__Nocardioides sp013177455	83.7758	919	1402	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	83.4758	892	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	83.3929	912	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003710085.1	s__Nocardioides sp003710085	83.2421	890	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	82.8261	811	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_015024225.1	s__Nocardioides sp015024225	82.7838	872	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_014212315.1	s__Nocardioides luti	82.7781	835	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522095.1	s__Nocardioides sp004522095	82.6205	862	1402	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	82.5459	857	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	82.4965	846	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	82.4837	797	1402	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	82.4138	871	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907435.1	s__Nocardioides salarius	82.3984	846	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015070375.1	s__Nocardioides kribbensis	82.3581	811	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCA_001627335.1	s__Nocardioides sp001627335	81.858	700	1402	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_008087085.1	s__Nocardioides rubriscoriae	81.5514	837	1402	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 10:49:12,373] [INFO] GTDB search result was written to GCF_014127485.1_ASM1412748v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:12,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:12,377] [INFO] DFAST_QC result json was written to GCF_014127485.1_ASM1412748v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:12,378] [INFO] DFAST_QC completed!
[2024-01-24 10:49:12,378] [INFO] Total running time: 0h2m6s