[2023-06-27 05:46:11,246] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:46:11,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:46:11,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference
[2023-06-27 05:46:12,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:46:12,660] [INFO] Task started: Prodigal
[2023-06-27 05:46:12,660] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2a6fe88-b127-47ae-bc7c-5a0d7f65c094/GCA_026392455.1_ASM2639245v1_genomic.fna.gz | prodigal -d GCA_026392455.1_ASM2639245v1_genomic.fna/cds.fna -a GCA_026392455.1_ASM2639245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:46:22,621] [INFO] Task succeeded: Prodigal
[2023-06-27 05:46:22,621] [INFO] Task started: HMMsearch
[2023-06-27 05:46:22,621] [INFO] Running command: hmmsearch --tblout GCA_026392455.1_ASM2639245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference/reference_markers.hmm GCA_026392455.1_ASM2639245v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:46:22,939] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:46:22,941] [INFO] Found 6/6 markers.
[2023-06-27 05:46:22,974] [INFO] Query marker FASTA was written to GCA_026392455.1_ASM2639245v1_genomic.fna/markers.fasta
[2023-06-27 05:46:22,975] [INFO] Task started: Blastn
[2023-06-27 05:46:22,975] [INFO] Running command: blastn -query GCA_026392455.1_ASM2639245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference/reference_markers.fasta -out GCA_026392455.1_ASM2639245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:46:24,244] [INFO] Task succeeded: Blastn
[2023-06-27 05:46:24,248] [INFO] Selected 23 target genomes.
[2023-06-27 05:46:24,249] [INFO] Target genome list was writen to GCA_026392455.1_ASM2639245v1_genomic.fna/target_genomes.txt
[2023-06-27 05:46:24,254] [INFO] Task started: fastANI
[2023-06-27 05:46:24,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a6fe88-b127-47ae-bc7c-5a0d7f65c094/GCA_026392455.1_ASM2639245v1_genomic.fna.gz --refList GCA_026392455.1_ASM2639245v1_genomic.fna/target_genomes.txt --output GCA_026392455.1_ASM2639245v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:46:44,492] [INFO] Task succeeded: fastANI
[2023-06-27 05:46:44,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:46:44,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:46:44,517] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:46:44,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:46:44,517] [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
Marmoricola ginsengisoli	strain=Gsoil 097	GCA_003725695.1	661483	661483	type	True	83.7471	841	1179	95	below_threshold
Marmoricola solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	82.7175	810	1179	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	79.8226	552	1179	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.7775	545	1179	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	79.7691	567	1179	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	79.6797	569	1179	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.5909	496	1179	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.5845	473	1179	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.5759	571	1179	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.5636	575	1179	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	79.5295	516	1179	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	79.3867	485	1179	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	79.3629	498	1179	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	79.352	538	1179	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.333	475	1179	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.307	530	1179	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.241	538	1179	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	79.2246	437	1179	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	79.2022	475	1179	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.1136	483	1179	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	79.094	546	1179	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.0062	475	1179	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	78.8282	463	1179	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:46:44,534] [INFO] DFAST Taxonomy check result was written to GCA_026392455.1_ASM2639245v1_genomic.fna/tc_result.tsv
[2023-06-27 05:46:44,535] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:46:44,535] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:46:44,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference/checkm_data
[2023-06-27 05:46:44,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:46:44,577] [INFO] Task started: CheckM
[2023-06-27 05:46:44,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026392455.1_ASM2639245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026392455.1_ASM2639245v1_genomic.fna/checkm_input GCA_026392455.1_ASM2639245v1_genomic.fna/checkm_result
[2023-06-27 05:47:29,525] [INFO] Task succeeded: CheckM
[2023-06-27 05:47:29,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:47:29,544] [INFO] ===== Completeness check finished =====
[2023-06-27 05:47:29,544] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:47:29,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026392455.1_ASM2639245v1_genomic.fna/markers.fasta)
[2023-06-27 05:47:29,545] [INFO] Task started: Blastn
[2023-06-27 05:47:29,545] [INFO] Running command: blastn -query GCA_026392455.1_ASM2639245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg900bb61b-2f3b-4619-9259-83f6f61dda8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026392455.1_ASM2639245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:47:31,376] [INFO] Task succeeded: Blastn
[2023-06-27 05:47:31,381] [INFO] Selected 13 target genomes.
[2023-06-27 05:47:31,381] [INFO] Target genome list was writen to GCA_026392455.1_ASM2639245v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:47:31,396] [INFO] Task started: fastANI
[2023-06-27 05:47:31,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a6fe88-b127-47ae-bc7c-5a0d7f65c094/GCA_026392455.1_ASM2639245v1_genomic.fna.gz --refList GCA_026392455.1_ASM2639245v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026392455.1_ASM2639245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:47:43,237] [INFO] Task succeeded: fastANI
[2023-06-27 05:47:43,253] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 05:47:43,253] [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_003725695.1	s__Marmoricola ginsengisoli	83.7581	840	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872665.1	s__Marmoricola sp017872665	83.5098	896	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725775.1	s__Marmoricola solisilvae	82.7077	811	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744365.1	s__Marmoricola sp017744365	81.8575	763	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	81.0985	696	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426045.1	s__Marmoricola sp000426045	79.8674	592	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	79.7848	565	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_003752505.1	s__Marmoricola aurantiacus	79.7442	549	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	79.7127	599	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	79.6425	491	1179	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	79.5823	564	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	79.5552	573	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014395785.1	s__Nocardioides_B mesophilus	79.3796	481	1179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:47:43,264] [INFO] GTDB search result was written to GCA_026392455.1_ASM2639245v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:47:43,265] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:47:43,272] [INFO] DFAST_QC result json was written to GCA_026392455.1_ASM2639245v1_genomic.fna/dqc_result.json
[2023-06-27 05:47:43,273] [INFO] DFAST_QC completed!
[2023-06-27 05:47:43,273] [INFO] Total running time: 0h1m32s