[2024-01-24 13:57:42,817] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,819] [INFO] DQC Reference Directory: /var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference
[2024-01-24 13:57:44,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,044] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,044] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f48eee-0f8d-4645-ae25-0e58fa2ae49f/GCF_003600895.1_ASM360089v1_genomic.fna.gz | prodigal -d GCF_003600895.1_ASM360089v1_genomic.fna/cds.fna -a GCF_003600895.1_ASM360089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:54,253] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:54,253] [INFO] Task started: HMMsearch
[2024-01-24 13:57:54,253] [INFO] Running command: hmmsearch --tblout GCF_003600895.1_ASM360089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference/reference_markers.hmm GCF_003600895.1_ASM360089v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:54,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:54,532] [INFO] Found 6/6 markers.
[2024-01-24 13:57:54,571] [INFO] Query marker FASTA was written to GCF_003600895.1_ASM360089v1_genomic.fna/markers.fasta
[2024-01-24 13:57:54,572] [INFO] Task started: Blastn
[2024-01-24 13:57:54,572] [INFO] Running command: blastn -query GCF_003600895.1_ASM360089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference/reference_markers.fasta -out GCF_003600895.1_ASM360089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,832] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,837] [INFO] Selected 23 target genomes.
[2024-01-24 13:57:55,837] [INFO] Target genome list was writen to GCF_003600895.1_ASM360089v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:55,847] [INFO] Task started: fastANI
[2024-01-24 13:57:55,847] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f48eee-0f8d-4645-ae25-0e58fa2ae49f/GCF_003600895.1_ASM360089v1_genomic.fna.gz --refList GCF_003600895.1_ASM360089v1_genomic.fna/target_genomes.txt --output GCF_003600895.1_ASM360089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:15,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:15,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:15,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:15,484] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:15,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:15,485] [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 cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	100.0	1152	1154	95	conclusive
Nocardioides phosphati	strain=CGMCC 4.7371	GCA_014646375.1	1867775	1867775	type	True	83.2494	732	1154	95	below_threshold
Nocardioides jejuensis	strain=18JY15-6	GCA_004337475.1	2502782	2502782	type	True	82.8439	711	1154	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.6949	542	1154	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.3226	572	1154	95	below_threshold
Nocardioides jensenii	strain=NBRC 14755	GCA_001552535.1	1843	1843	type	True	80.2222	551	1154	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.1713	530	1154	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	80.1542	540	1154	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	80.0691	484	1154	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.067	558	1154	95	below_threshold
Nocardioides daedukensis	strain=DSM 23819	GCA_013408415.1	634462	634462	type	True	80.0577	468	1154	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.0006	554	1154	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	79.9389	523	1154	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.9387	540	1154	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	79.9382	523	1154	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.9225	512	1154	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.9151	530	1154	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	79.8543	543	1154	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.8412	537	1154	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	79.8344	450	1154	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	79.7826	512	1154	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.7443	553	1154	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	79.6621	544	1154	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:15,487] [INFO] DFAST Taxonomy check result was written to GCF_003600895.1_ASM360089v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:15,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:15,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:15,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference/checkm_data
[2024-01-24 13:58:15,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:15,525] [INFO] Task started: CheckM
[2024-01-24 13:58:15,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003600895.1_ASM360089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003600895.1_ASM360089v1_genomic.fna/checkm_input GCF_003600895.1_ASM360089v1_genomic.fna/checkm_result
[2024-01-24 13:59:17,210] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:17,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,233] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:17,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:17,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003600895.1_ASM360089v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:17,234] [INFO] Task started: Blastn
[2024-01-24 13:59:17,234] [INFO] Running command: blastn -query GCF_003600895.1_ASM360089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfff31584-0eec-46cf-a239-07ee60660ca3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003600895.1_ASM360089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:19,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:19,177] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:19,178] [INFO] Target genome list was writen to GCF_003600895.1_ASM360089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:19,196] [INFO] Task started: fastANI
[2024-01-24 13:59:19,196] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f48eee-0f8d-4645-ae25-0e58fa2ae49f/GCF_003600895.1_ASM360089v1_genomic.fna.gz --refList GCF_003600895.1_ASM360089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003600895.1_ASM360089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:34,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:34,553] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:34,553] [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_003600895.1	s__Nocardioides sp003600895	100.0	1150	1154	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_014646375.1	s__Nocardioides phosphati	83.2702	730	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053885.1	s__Nocardioides sp003053885	83.0762	727	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337475.1	s__Nocardioides jejuensis	82.8448	712	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.6947	542	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_014212315.1	s__Nocardioides luti	80.3368	571	1154	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	80.1449	534	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003057875.1	s__Nocardioides currus	80.1425	541	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.1179	541	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	80.0111	530	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	79.9979	553	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	79.9969	516	1154	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	79.9304	510	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	79.9135	524	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCA_001627335.1	s__Nocardioides sp001627335	79.9041	462	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_014191495.1	s__Nocardioides soli	79.839	533	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_017310035.1	s__Nocardioides sp017310035	79.7972	540	1154	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	79.5897	520	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213595.1	s__Fen-668 sp016213595	77.083	125	1154	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:34,555] [INFO] GTDB search result was written to GCF_003600895.1_ASM360089v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:34,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:34,562] [INFO] DFAST_QC result json was written to GCF_003600895.1_ASM360089v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:34,563] [INFO] DFAST_QC completed!
[2024-01-24 13:59:34,563] [INFO] Total running time: 0h1m52s