[2024-01-24 12:06:14,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,230] [INFO] DQC Reference Directory: /var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference
[2024-01-24 12:06:15,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,684] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg07f758c7-d1c3-4c80-9cc5-4604510d995d/GCF_014842875.1_ASM1484287v1_genomic.fna.gz | prodigal -d GCF_014842875.1_ASM1484287v1_genomic.fna/cds.fna -a GCF_014842875.1_ASM1484287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,177] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,178] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,178] [INFO] Running command: hmmsearch --tblout GCF_014842875.1_ASM1484287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference/reference_markers.hmm GCF_014842875.1_ASM1484287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,494] [INFO] Found 6/6 markers.
[2024-01-24 12:06:25,533] [INFO] Query marker FASTA was written to GCF_014842875.1_ASM1484287v1_genomic.fna/markers.fasta
[2024-01-24 12:06:25,534] [INFO] Task started: Blastn
[2024-01-24 12:06:25,534] [INFO] Running command: blastn -query GCF_014842875.1_ASM1484287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference/reference_markers.fasta -out GCF_014842875.1_ASM1484287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,823] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,836] [INFO] Selected 24 target genomes.
[2024-01-24 12:06:26,836] [INFO] Target genome list was writen to GCF_014842875.1_ASM1484287v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,846] [INFO] Task started: fastANI
[2024-01-24 12:06:26,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f758c7-d1c3-4c80-9cc5-4604510d995d/GCF_014842875.1_ASM1484287v1_genomic.fna.gz --refList GCF_014842875.1_ASM1484287v1_genomic.fna/target_genomes.txt --output GCF_014842875.1_ASM1484287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:50,701] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:50,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:50,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:50,721] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:50,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:50,721] [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 donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	100.0	1135	1135	95	conclusive
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	82.1943	758	1135	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.4601	687	1135	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	81.3871	671	1135	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.1081	679	1135	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.0378	688	1135	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.9252	695	1135	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	80.8997	680	1135	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.8615	639	1135	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	80.8478	640	1135	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	80.8352	635	1135	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.805	667	1135	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.6623	638	1135	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	80.6523	641	1135	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.5381	680	1135	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	80.518	577	1135	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.4119	664	1135	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.3198	632	1135	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	80.1843	649	1135	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	80.059	652	1135	95	below_threshold
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	79.8012	516	1135	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.7111	591	1135	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	79.5453	605	1135	95	below_threshold
Nocardioides jejuensis	strain=18JY15-6	GCA_004337475.1	2502782	2502782	type	True	79.5282	469	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:50,724] [INFO] DFAST Taxonomy check result was written to GCF_014842875.1_ASM1484287v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:50,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:50,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:50,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference/checkm_data
[2024-01-24 12:06:50,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:50,767] [INFO] Task started: CheckM
[2024-01-24 12:06:50,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014842875.1_ASM1484287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014842875.1_ASM1484287v1_genomic.fna/checkm_input GCF_014842875.1_ASM1484287v1_genomic.fna/checkm_result
[2024-01-24 12:07:42,853] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:42,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:42,874] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:42,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:42,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014842875.1_ASM1484287v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:42,876] [INFO] Task started: Blastn
[2024-01-24 12:07:42,876] [INFO] Running command: blastn -query GCF_014842875.1_ASM1484287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga514b72f-8e7d-4f8b-a1dc-74b4c46d5246/dqc_reference/reference_markers_gtdb.fasta -out GCF_014842875.1_ASM1484287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:44,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:44,823] [INFO] Selected 23 target genomes.
[2024-01-24 12:07:44,823] [INFO] Target genome list was writen to GCF_014842875.1_ASM1484287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:44,842] [INFO] Task started: fastANI
[2024-01-24 12:07:44,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f758c7-d1c3-4c80-9cc5-4604510d995d/GCF_014842875.1_ASM1484287v1_genomic.fna.gz --refList GCF_014842875.1_ASM1484287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014842875.1_ASM1484287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:07,231] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:07,253] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:07,253] [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_014842875.1	s__Nocardioides sp014842875	100.0	1135	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004519545.1	s__Nocardioides guangzhouensis	82.2249	755	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.558	678	1135	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	81.1501	675	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003710085.1	s__Nocardioides sp003710085	81.0394	626	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_001426745.1	s__Nocardioides sp001426745	81.018	681	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.99	98.75	0.96	0.95	3	-
GCF_014212315.1	s__Nocardioides luti	80.9405	693	1135	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	80.9397	657	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_014266025.1	s__Nocardioides deserti	80.9011	635	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	80.84	635	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	80.8259	643	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272695.1	s__Nocardioides sp012272695	80.7663	616	1135	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	80.721	660	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003121585.1	s__Nocardioides speluncae	80.7024	654	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	80.6737	685	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	80.6307	670	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014191495.1	s__Nocardioides soli	80.5367	671	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	80.509	683	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194625.1	s__Nocardioides solisilvae	80.4735	581	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155335.1	s__Nocardioides sp013155335	80.2325	638	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916425.1	s__Nocardioides sp017916425	80.15	580	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646375.1	s__Nocardioides phosphati	79.8064	515	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426525.1	s__Nocardioides alkalitolerans	79.5341	607	1135	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 12:08:07,255] [INFO] GTDB search result was written to GCF_014842875.1_ASM1484287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:07,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:07,263] [INFO] DFAST_QC result json was written to GCF_014842875.1_ASM1484287v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:07,263] [INFO] DFAST_QC completed!
[2024-01-24 12:08:07,263] [INFO] Total running time: 0h1m53s