[2024-01-24 12:14:33,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,968] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference
[2024-01-24 12:14:35,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,150] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,150] [INFO] Running command: gunzip -c /var/lib/cwl/stge05ac3e0-3d9c-4368-9411-3f9f1ddb40d5/GCF_003515065.1_ASM351506v1_genomic.fna.gz | prodigal -d GCF_003515065.1_ASM351506v1_genomic.fna/cds.fna -a GCF_003515065.1_ASM351506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:51,034] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:51,034] [INFO] Task started: HMMsearch
[2024-01-24 12:14:51,034] [INFO] Running command: hmmsearch --tblout GCF_003515065.1_ASM351506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference/reference_markers.hmm GCF_003515065.1_ASM351506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:51,426] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:51,427] [INFO] Found 6/6 markers.
[2024-01-24 12:14:51,477] [INFO] Query marker FASTA was written to GCF_003515065.1_ASM351506v1_genomic.fna/markers.fasta
[2024-01-24 12:14:51,477] [INFO] Task started: Blastn
[2024-01-24 12:14:51,477] [INFO] Running command: blastn -query GCF_003515065.1_ASM351506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference/reference_markers.fasta -out GCF_003515065.1_ASM351506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:52,643] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:52,646] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:52,647] [INFO] Target genome list was writen to GCF_003515065.1_ASM351506v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:52,666] [INFO] Task started: fastANI
[2024-01-24 12:14:52,666] [INFO] Running command: fastANI --query /var/lib/cwl/stge05ac3e0-3d9c-4368-9411-3f9f1ddb40d5/GCF_003515065.1_ASM351506v1_genomic.fna.gz --refList GCF_003515065.1_ASM351506v1_genomic.fna/target_genomes.txt --output GCF_003515065.1_ASM351506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:06,560] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:06,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:06,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:06,571] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:06,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:06,571] [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 immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	100.0	2134	2135	95	conclusive
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	86.03	1085	2135	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	85.748	970	2135	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	84.4442	1065	2135	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	83.7726	955	2135	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	83.3744	1007	2135	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.9081	899	2135	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.7498	801	2135	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.2368	749	2135	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.8159	583	2135	95	below_threshold
Nocardioides terrae	strain=CGMCC 1.7056	GCA_900112345.1	574651	574651	type	True	79.6113	631	2135	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.4214	596	2135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,572] [INFO] DFAST Taxonomy check result was written to GCF_003515065.1_ASM351506v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:06,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:06,573] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:06,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference/checkm_data
[2024-01-24 12:15:06,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:06,637] [INFO] Task started: CheckM
[2024-01-24 12:15:06,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003515065.1_ASM351506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003515065.1_ASM351506v1_genomic.fna/checkm_input GCF_003515065.1_ASM351506v1_genomic.fna/checkm_result
[2024-01-24 12:16:24,680] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:24,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:24,695] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:24,695] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:24,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003515065.1_ASM351506v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:24,696] [INFO] Task started: Blastn
[2024-01-24 12:16:24,696] [INFO] Running command: blastn -query GCF_003515065.1_ASM351506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39f2a826-ffd2-4b7c-9658-afe8a5f6d015/dqc_reference/reference_markers_gtdb.fasta -out GCF_003515065.1_ASM351506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:26,593] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:26,597] [INFO] Selected 8 target genomes.
[2024-01-24 12:16:26,597] [INFO] Target genome list was writen to GCF_003515065.1_ASM351506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:26,602] [INFO] Task started: fastANI
[2024-01-24 12:16:26,602] [INFO] Running command: fastANI --query /var/lib/cwl/stge05ac3e0-3d9c-4368-9411-3f9f1ddb40d5/GCF_003515065.1_ASM351506v1_genomic.fna.gz --refList GCF_003515065.1_ASM351506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003515065.1_ASM351506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:36,645] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:36,651] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:36,651] [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_003515065.1	s__Nocardioides immobilis	100.0	2134	2135	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_008373765.1	s__Nocardioides antri	86.0004	1088	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180685.1	s__Nocardioides pelophilus	85.7104	974	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003160695.1	s__Nocardioides silvaticus	84.4666	1063	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180715.1	s__Nocardioides stalactiti	83.7827	954	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008373755.1	s__Nocardioides sp008373755	83.3627	1008	2135	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	80.5405	756	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900112345.1	s__Nocardioides terrae	79.6172	630	2135	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 12:16:36,652] [INFO] GTDB search result was written to GCF_003515065.1_ASM351506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:36,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:36,655] [INFO] DFAST_QC result json was written to GCF_003515065.1_ASM351506v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:36,655] [INFO] DFAST_QC completed!
[2024-01-24 12:16:36,655] [INFO] Total running time: 0h2m3s