[2024-01-25 17:39:50,457] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:50,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:50,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference
[2024-01-25 17:39:51,605] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:51,606] [INFO] Task started: Prodigal
[2024-01-25 17:39:51,606] [INFO] Running command: gunzip -c /var/lib/cwl/stga9c35ddf-5769-4e09-ae7f-5bd5c14d5b3a/GCF_014191915.1_ASM1419191v1_genomic.fna.gz | prodigal -d GCF_014191915.1_ASM1419191v1_genomic.fna/cds.fna -a GCF_014191915.1_ASM1419191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:05,589] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:05,589] [INFO] Task started: HMMsearch
[2024-01-25 17:40:05,589] [INFO] Running command: hmmsearch --tblout GCF_014191915.1_ASM1419191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference/reference_markers.hmm GCF_014191915.1_ASM1419191v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:05,870] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:05,871] [INFO] Found 6/6 markers.
[2024-01-25 17:40:05,919] [INFO] Query marker FASTA was written to GCF_014191915.1_ASM1419191v1_genomic.fna/markers.fasta
[2024-01-25 17:40:05,920] [INFO] Task started: Blastn
[2024-01-25 17:40:05,920] [INFO] Running command: blastn -query GCF_014191915.1_ASM1419191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference/reference_markers.fasta -out GCF_014191915.1_ASM1419191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:07,034] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:07,036] [INFO] Selected 13 target genomes.
[2024-01-25 17:40:07,037] [INFO] Target genome list was writen to GCF_014191915.1_ASM1419191v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:07,048] [INFO] Task started: fastANI
[2024-01-25 17:40:07,048] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c35ddf-5769-4e09-ae7f-5bd5c14d5b3a/GCF_014191915.1_ASM1419191v1_genomic.fna.gz --refList GCF_014191915.1_ASM1419191v1_genomic.fna/target_genomes.txt --output GCF_014191915.1_ASM1419191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:22,325] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:22,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:22,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:22,335] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:22,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:22,335] [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 albus	strain=JCM 3185	GCA_014648255.1	1841	1841	type	True	99.9932	1857	1869	95	conclusive
Nocardioides panzhihuensis	strain=DSM 26487	GCA_013408335.1	860243	860243	type	True	91.5108	1514	1869	95	below_threshold
Nocardioides luteus	strain=JCM 3358	GCA_014648595.1	1844	1844	type	True	88.2214	1317	1869	95	below_threshold
Nocardioides albertanoniae	strain=DSM 25218	GCA_006716315.1	1175486	1175486	type	True	86.9994	1288	1869	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	79.9977	623	1869	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	79.3843	621	1869	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.3418	665	1869	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.2308	694	1869	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	79.1253	629	1869	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.1162	700	1869	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.1119	634	1869	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.0977	634	1869	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.0833	589	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:22,337] [INFO] DFAST Taxonomy check result was written to GCF_014191915.1_ASM1419191v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:22,337] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:22,337] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:22,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference/checkm_data
[2024-01-25 17:40:22,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:22,391] [INFO] Task started: CheckM
[2024-01-25 17:40:22,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191915.1_ASM1419191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191915.1_ASM1419191v1_genomic.fna/checkm_input GCF_014191915.1_ASM1419191v1_genomic.fna/checkm_result
[2024-01-25 17:41:11,189] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:11,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:11,207] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:11,207] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:11,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191915.1_ASM1419191v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:11,208] [INFO] Task started: Blastn
[2024-01-25 17:41:11,208] [INFO] Running command: blastn -query GCF_014191915.1_ASM1419191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg374178bf-8898-473d-9b14-4f8f133d83f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191915.1_ASM1419191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:13,034] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:13,036] [INFO] Selected 11 target genomes.
[2024-01-25 17:41:13,037] [INFO] Target genome list was writen to GCF_014191915.1_ASM1419191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:13,049] [INFO] Task started: fastANI
[2024-01-25 17:41:13,049] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c35ddf-5769-4e09-ae7f-5bd5c14d5b3a/GCF_014191915.1_ASM1419191v1_genomic.fna.gz --refList GCF_014191915.1_ASM1419191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191915.1_ASM1419191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:30,359] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:30,367] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:30,367] [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_014648255.1	s__Nocardioides albus	99.9932	1857	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013408335.1	s__Nocardioides panzhihuensis	91.4982	1515	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014360585.1	s__Nocardioides sp014360585	91.2384	1401	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858265.1	s__Nocardioides sp009858265	90.3494	1478	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715835.1	s__Nocardioides sp006715835	90.3161	1490	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101045.1	s__Nocardioides sp900101045	89.947	1474	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752315.1	s__Nocardioides sp000192415	89.6846	1443	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.29	98.29	0.91	0.91	2	-
GCF_000960475.2	s__Nocardioides luteus_A	89.5704	1396	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045035.1	s__Nocardioides sp011045035	89.5647	1393	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715515.1	s__Nocardioides sp006715515	89.5476	1431	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648595.1	s__Nocardioides luteus	88.2433	1315	1869	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:30,369] [INFO] GTDB search result was written to GCF_014191915.1_ASM1419191v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:30,369] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:30,372] [INFO] DFAST_QC result json was written to GCF_014191915.1_ASM1419191v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:30,373] [INFO] DFAST_QC completed!
[2024-01-25 17:41:30,373] [INFO] Total running time: 0h1m40s