[2024-01-24 13:55:47,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:47,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:47,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference
[2024-01-24 13:55:48,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:48,378] [INFO] Task started: Prodigal
[2024-01-24 13:55:48,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a9fa56e-c275-4c2f-9acb-0f9bd8504c13/GCF_014841105.1_ASM1484110v1_genomic.fna.gz | prodigal -d GCF_014841105.1_ASM1484110v1_genomic.fna/cds.fna -a GCF_014841105.1_ASM1484110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:00,360] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:00,360] [INFO] Task started: HMMsearch
[2024-01-24 13:56:00,360] [INFO] Running command: hmmsearch --tblout GCF_014841105.1_ASM1484110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference/reference_markers.hmm GCF_014841105.1_ASM1484110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:00,618] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:00,620] [INFO] Found 6/6 markers.
[2024-01-24 13:56:00,652] [INFO] Query marker FASTA was written to GCF_014841105.1_ASM1484110v1_genomic.fna/markers.fasta
[2024-01-24 13:56:00,652] [INFO] Task started: Blastn
[2024-01-24 13:56:00,652] [INFO] Running command: blastn -query GCF_014841105.1_ASM1484110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference/reference_markers.fasta -out GCF_014841105.1_ASM1484110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:01,764] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:01,769] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:01,769] [INFO] Target genome list was writen to GCF_014841105.1_ASM1484110v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:01,780] [INFO] Task started: fastANI
[2024-01-24 13:56:01,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9fa56e-c275-4c2f-9acb-0f9bd8504c13/GCF_014841105.1_ASM1484110v1_genomic.fna.gz --refList GCF_014841105.1_ASM1484110v1_genomic.fna/target_genomes.txt --output GCF_014841105.1_ASM1484110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:17,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:17,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:17,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:17,315] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:17,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:17,315] [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
Hoyosella lacisalsi	strain=G463	GCA_014841105.1	2742202	2742202	type	True	100.0	1138	1139	95	conclusive
Hoyosella suaedae	strain=LNNU 331112	GCA_008312885.1	2605429	2605429	type	True	89.3509	1029	1139	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.0227	349	1139	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	77.9899	373	1139	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	77.9816	361	1139	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	77.9216	345	1139	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	77.8855	353	1139	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	77.8566	315	1139	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	77.8521	330	1139	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	77.7491	339	1139	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	77.5639	370	1139	95	below_threshold
Hoyosella altamirensis	strain=DSM 45258	GCA_014191505.1	616997	616997	type	True	77.5627	269	1139	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	77.5149	377	1139	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	76.8801	252	1139	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	76.7039	277	1139	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	76.3883	171	1139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:17,322] [INFO] DFAST Taxonomy check result was written to GCF_014841105.1_ASM1484110v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:17,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:17,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:17,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference/checkm_data
[2024-01-24 13:56:17,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:17,361] [INFO] Task started: CheckM
[2024-01-24 13:56:17,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014841105.1_ASM1484110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014841105.1_ASM1484110v1_genomic.fna/checkm_input GCF_014841105.1_ASM1484110v1_genomic.fna/checkm_result
[2024-01-24 13:56:54,585] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:54,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:54,608] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:54,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:54,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014841105.1_ASM1484110v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:54,609] [INFO] Task started: Blastn
[2024-01-24 13:56:54,609] [INFO] Running command: blastn -query GCF_014841105.1_ASM1484110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg858947dc-40f8-4bee-95a7-415bcc7468a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014841105.1_ASM1484110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:56,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:56,179] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:56,179] [INFO] Target genome list was writen to GCF_014841105.1_ASM1484110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:56,250] [INFO] Task started: fastANI
[2024-01-24 13:56:56,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a9fa56e-c275-4c2f-9acb-0f9bd8504c13/GCF_014841105.1_ASM1484110v1_genomic.fna.gz --refList GCF_014841105.1_ASM1484110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014841105.1_ASM1484110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:12,355] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:12,377] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:12,377] [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_014841105.1	s__Hoyosella sp014841105	100.0	1138	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008312885.1	s__Hoyosella sp008312885	89.3509	1029	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006704125.1	s__Rhodococcus sp006704125	78.0859	333	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005049235.1	s__Rhodococcus oryzae	78.0281	346	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_001894865.1	s__Rhodococcus maanshanensis	77.989	361	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_001613125.1	s__Nocardia shimofusensis	77.9761	345	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187265.1	s__Rhodococcus rhodochrous	77.906	349	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
GCF_015477835.1	s__Nocardia higoensis_A	77.8747	329	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	77.7353	339	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738775.1	s__Rhodococcus defluvii	77.7072	316	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003051005.1	s__Rhodococcus sp003051005	77.6938	312	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014565.1	s__Rhodococcus jostii_A	77.6538	331	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_014191505.1	s__Hoyosella altamirensis	77.5512	270	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	99.98	99.98	0.97	0.97	2	-
GCF_015477355.1	s__Nocardia blacklockiae	77.5438	377	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911875.1	s__Pseudonocardia bannensis	76.878	251	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911935.1	s__Pseudonocardia sp012911935	76.718	275	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848795.1	s__JAFIHG01 sp017848795	76.2173	124	1139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__JAFIHG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:12,379] [INFO] GTDB search result was written to GCF_014841105.1_ASM1484110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:12,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:12,386] [INFO] DFAST_QC result json was written to GCF_014841105.1_ASM1484110v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:12,387] [INFO] DFAST_QC completed!
[2024-01-24 13:57:12,387] [INFO] Total running time: 0h1m25s