[2024-01-24 14:30:59,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference
[2024-01-24 14:31:00,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,832] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgafa342a2-9fe6-4ee5-845e-048e376f71ff/GCF_013410655.1_ASM1341065v1_genomic.fna.gz | prodigal -d GCF_013410655.1_ASM1341065v1_genomic.fna/cds.fna -a GCF_013410655.1_ASM1341065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:14,215] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:14,216] [INFO] Task started: HMMsearch
[2024-01-24 14:31:14,216] [INFO] Running command: hmmsearch --tblout GCF_013410655.1_ASM1341065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference/reference_markers.hmm GCF_013410655.1_ASM1341065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:14,566] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:14,567] [INFO] Found 6/6 markers.
[2024-01-24 14:31:14,622] [INFO] Query marker FASTA was written to GCF_013410655.1_ASM1341065v1_genomic.fna/markers.fasta
[2024-01-24 14:31:14,623] [INFO] Task started: Blastn
[2024-01-24 14:31:14,623] [INFO] Running command: blastn -query GCF_013410655.1_ASM1341065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference/reference_markers.fasta -out GCF_013410655.1_ASM1341065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:16,027] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:16,031] [INFO] Selected 23 target genomes.
[2024-01-24 14:31:16,031] [INFO] Target genome list was writen to GCF_013410655.1_ASM1341065v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:16,040] [INFO] Task started: fastANI
[2024-01-24 14:31:16,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgafa342a2-9fe6-4ee5-845e-048e376f71ff/GCF_013410655.1_ASM1341065v1_genomic.fna.gz --refList GCF_013410655.1_ASM1341065v1_genomic.fna/target_genomes.txt --output GCF_013410655.1_ASM1341065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:46,078] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:46,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:46,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:46,097] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:46,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:46,098] [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 thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	100.0	1523	1523	95	conclusive
Nocardioides antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	82.7432	861	1523	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	82.729	929	1523	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	82.4823	784	1523	95	below_threshold
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	82.3581	910	1523	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	82.2887	811	1523	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	82.0954	927	1523	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	81.9794	832	1523	95	below_threshold
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	81.9147	915	1523	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	81.7845	925	1523	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	81.772	932	1523	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.7675	849	1523	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	81.6764	947	1523	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	81.5856	873	1523	95	below_threshold
Nocardioides caeni	strain=DSM 23134	GCA_004912195.1	574700	574700	type	True	81.557	805	1523	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.0199	777	1523	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.7771	763	1523	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	80.7005	795	1523	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.5636	840	1523	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.4863	837	1523	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	80.4489	763	1523	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.9657	689	1523	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.7913	626	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:46,100] [INFO] DFAST Taxonomy check result was written to GCF_013410655.1_ASM1341065v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:46,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:46,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:46,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference/checkm_data
[2024-01-24 14:31:46,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:46,149] [INFO] Task started: CheckM
[2024-01-24 14:31:46,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410655.1_ASM1341065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410655.1_ASM1341065v1_genomic.fna/checkm_input GCF_013410655.1_ASM1341065v1_genomic.fna/checkm_result
[2024-01-24 14:32:50,748] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:50,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:50,769] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:50,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:50,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410655.1_ASM1341065v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:50,771] [INFO] Task started: Blastn
[2024-01-24 14:32:50,771] [INFO] Running command: blastn -query GCF_013410655.1_ASM1341065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab775681-4fdb-460c-8ddb-2bddc56f8a5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410655.1_ASM1341065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:52,730] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:52,735] [INFO] Selected 23 target genomes.
[2024-01-24 14:32:52,736] [INFO] Target genome list was writen to GCF_013410655.1_ASM1341065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:52,753] [INFO] Task started: fastANI
[2024-01-24 14:32:52,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgafa342a2-9fe6-4ee5-845e-048e376f71ff/GCF_013410655.1_ASM1341065v1_genomic.fna.gz --refList GCF_013410655.1_ASM1341065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410655.1_ASM1341065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:19,432] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:19,450] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:19,450] [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_013410655.1	s__Nocardioides thalensis	100.0	1523	1523	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	82.772	858	1523	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	82.7268	930	1523	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	82.4531	788	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515065.1	s__Nocardioides immobilis	82.3845	906	1523	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	82.2888	811	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	82.2569	867	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_014873635.1	s__Nocardioides sp014873635	82.0802	917	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408525.1	s__Nocardioides aromaticivorans	82.0788	929	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
GCF_016803235.1	s__Nocardioides simplex_A	82.0559	890	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054165.1	s__Nocardioides sp003054165	81.9635	898	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	81.9445	928	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	81.9244	902	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803405.1	s__Nocardioides sp004803405	81.8134	722	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	81.7819	932	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
GCF_004919105.1	s__Nocardioides sp004919105	81.4269	781	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924665.1	s__Nocardioides sp016924665	81.0311	777	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	80.8173	752	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015024225.1	s__Nocardioides sp015024225	80.7213	794	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	97.48	0.91	0.91	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.6669	812	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	80.44	844	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006346315.1	s__Nocardioides litoris	80.4142	767	1523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873835.1	s__Nocardioides sp014873835	80.0701	685	1523	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 14:33:19,452] [INFO] GTDB search result was written to GCF_013410655.1_ASM1341065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:19,452] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:19,457] [INFO] DFAST_QC result json was written to GCF_013410655.1_ASM1341065v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:19,457] [INFO] DFAST_QC completed!
[2024-01-24 14:33:19,457] [INFO] Total running time: 0h2m20s