[2024-01-24 12:07:06,590] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference
[2024-01-24 12:07:07,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,880] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,880] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d57c2db-4f79-4d32-823f-56b72cb2b39e/GCF_026008515.1_ASM2600851v1_genomic.fna.gz | prodigal -d GCF_026008515.1_ASM2600851v1_genomic.fna/cds.fna -a GCF_026008515.1_ASM2600851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:19,414] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:19,415] [INFO] Task started: HMMsearch
[2024-01-24 12:07:19,415] [INFO] Running command: hmmsearch --tblout GCF_026008515.1_ASM2600851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference/reference_markers.hmm GCF_026008515.1_ASM2600851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:19,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:19,710] [INFO] Found 6/6 markers.
[2024-01-24 12:07:19,742] [INFO] Query marker FASTA was written to GCF_026008515.1_ASM2600851v1_genomic.fna/markers.fasta
[2024-01-24 12:07:19,742] [INFO] Task started: Blastn
[2024-01-24 12:07:19,743] [INFO] Running command: blastn -query GCF_026008515.1_ASM2600851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference/reference_markers.fasta -out GCF_026008515.1_ASM2600851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:20,826] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:20,829] [INFO] Selected 20 target genomes.
[2024-01-24 12:07:20,830] [INFO] Target genome list was writen to GCF_026008515.1_ASM2600851v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:20,838] [INFO] Task started: fastANI
[2024-01-24 12:07:20,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d57c2db-4f79-4d32-823f-56b72cb2b39e/GCF_026008515.1_ASM2600851v1_genomic.fna.gz --refList GCF_026008515.1_ASM2600851v1_genomic.fna/target_genomes.txt --output GCF_026008515.1_ASM2600851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:38,538] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:38,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:38,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:38,559] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:38,560] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:38,560] [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 suaedae	strain=LNNU 331112	GCA_008312885.1	2605429	2605429	type	True	89.4693	1025	1189	95	below_threshold
Hoyosella lacisalsi	strain=G463	GCA_014841105.1	2742202	2742202	type	True	89.3426	1035	1189	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	78.2494	355	1189	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	78.236	375	1189	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	78.2104	354	1189	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	78.0085	377	1189	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	77.9799	367	1189	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	77.9773	370	1189	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	77.9713	329	1189	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	77.9654	359	1189	95	below_threshold
Nocardia higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	77.9369	346	1189	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	77.8438	325	1189	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	77.8143	323	1189	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	77.801	345	1189	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	77.024	208	1189	95	below_threshold
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	76.9992	209	1189	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	76.9595	257	1189	95	below_threshold
Pseudonocardia acidicola	strain=K10HN5	GCA_012911935.1	2724939	2724939	type	True	76.9154	260	1189	95	below_threshold
Halopolyspora algeriensis	strain=DSM 46680	GCA_006716575.1	1500506	1500506	type	True	76.5988	158	1189	95	below_threshold
Halopolyspora algeriensis	strain=CECT 8575	GCA_003337235.1	1500506	1500506	type	True	76.5606	162	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:38,575] [INFO] DFAST Taxonomy check result was written to GCF_026008515.1_ASM2600851v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:38,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:38,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:38,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference/checkm_data
[2024-01-24 12:07:38,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:38,614] [INFO] Task started: CheckM
[2024-01-24 12:07:38,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026008515.1_ASM2600851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026008515.1_ASM2600851v1_genomic.fna/checkm_input GCF_026008515.1_ASM2600851v1_genomic.fna/checkm_result
[2024-01-24 12:08:15,064] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:15,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:15,089] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:15,090] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:15,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026008515.1_ASM2600851v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:15,091] [INFO] Task started: Blastn
[2024-01-24 12:08:15,091] [INFO] Running command: blastn -query GCF_026008515.1_ASM2600851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c1de7c5-f773-4c59-954e-3060605f6294/dqc_reference/reference_markers_gtdb.fasta -out GCF_026008515.1_ASM2600851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:16,645] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:16,648] [INFO] Selected 18 target genomes.
[2024-01-24 12:08:16,648] [INFO] Target genome list was writen to GCF_026008515.1_ASM2600851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:16,663] [INFO] Task started: fastANI
[2024-01-24 12:08:16,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d57c2db-4f79-4d32-823f-56b72cb2b39e/GCF_026008515.1_ASM2600851v1_genomic.fna.gz --refList GCF_026008515.1_ASM2600851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026008515.1_ASM2600851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:34,832] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:34,851] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:08:34,851] [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_008312885.1	s__Hoyosella sp008312885	89.4693	1025	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841105.1	s__Hoyosella sp014841105	89.3426	1035	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	78.2247	358	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_005484805.1	s__Rhodococcus sp005484805	78.2058	335	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058165.1	s__Rhodococcus aetherivorans	78.1861	380	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_001894945.1	s__Rhodococcus ruber	78.0181	365	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	-
GCF_001894865.1	s__Rhodococcus maanshanensis	77.996	368	1189	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	77.9534	330	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005049235.1	s__Rhodococcus oryzae	77.9527	361	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_000308595.1	s__Nocardia higoensis	77.9424	348	1189	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	77.7629	349	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014565.1	s__Rhodococcus jostii_A	77.7153	335	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCA_002700145.1	s__Gordonia sp002700145	77.431	238	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	77.3138	211	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_008329905.1	s__Mycobacterium sp008329905	77.1135	212	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726245.1	s__Mycobacterium aichiense	76.9741	211	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012911935.1	s__Pseudonocardia sp012911935	76.8958	262	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001698125.1	s__Pseudonocardia sp001698125	76.5392	245	1189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:34,853] [INFO] GTDB search result was written to GCF_026008515.1_ASM2600851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:34,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:34,857] [INFO] DFAST_QC result json was written to GCF_026008515.1_ASM2600851v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:34,858] [INFO] DFAST_QC completed!
[2024-01-24 12:08:34,858] [INFO] Total running time: 0h1m28s