[2024-01-24 11:12:26,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:26,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:26,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference
[2024-01-24 11:12:27,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,888] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,888] [INFO] Running command: gunzip -c /var/lib/cwl/stg22ab8f5f-e9b8-434b-8ceb-03df107d9411/GCF_024171925.1_ASM2417192v1_genomic.fna.gz | prodigal -d GCF_024171925.1_ASM2417192v1_genomic.fna/cds.fna -a GCF_024171925.1_ASM2417192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:55,892] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:55,893] [INFO] Task started: HMMsearch
[2024-01-24 11:12:55,893] [INFO] Running command: hmmsearch --tblout GCF_024171925.1_ASM2417192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference/reference_markers.hmm GCF_024171925.1_ASM2417192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:56,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:56,407] [INFO] Found 6/6 markers.
[2024-01-24 11:12:56,466] [INFO] Query marker FASTA was written to GCF_024171925.1_ASM2417192v1_genomic.fna/markers.fasta
[2024-01-24 11:12:56,467] [INFO] Task started: Blastn
[2024-01-24 11:12:56,467] [INFO] Running command: blastn -query GCF_024171925.1_ASM2417192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference/reference_markers.fasta -out GCF_024171925.1_ASM2417192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:57,846] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:57,849] [INFO] Selected 10 target genomes.
[2024-01-24 11:12:57,850] [INFO] Target genome list was writen to GCF_024171925.1_ASM2417192v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:57,853] [INFO] Task started: fastANI
[2024-01-24 11:12:57,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg22ab8f5f-e9b8-434b-8ceb-03df107d9411/GCF_024171925.1_ASM2417192v1_genomic.fna.gz --refList GCF_024171925.1_ASM2417192v1_genomic.fna/target_genomes.txt --output GCF_024171925.1_ASM2417192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:23,512] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:23,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:23,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:23,522] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:23,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:23,523] [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
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	100.0	2687	2689	95	conclusive
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	89.9591	2158	2689	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	86.8485	1917	2689	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	86.7638	1896	2689	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	86.7003	1939	2689	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	84.1048	1600	2689	95	below_threshold
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	81.1047	1096	2689	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.3819	839	2689	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	78.1015	878	2689	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.9583	768	2689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,524] [INFO] DFAST Taxonomy check result was written to GCF_024171925.1_ASM2417192v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:23,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:23,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:23,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference/checkm_data
[2024-01-24 11:13:23,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:23,600] [INFO] Task started: CheckM
[2024-01-24 11:13:23,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171925.1_ASM2417192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171925.1_ASM2417192v1_genomic.fna/checkm_input GCF_024171925.1_ASM2417192v1_genomic.fna/checkm_result
[2024-01-24 11:14:45,465] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:45,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:45,492] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:45,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:45,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171925.1_ASM2417192v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:45,493] [INFO] Task started: Blastn
[2024-01-24 11:14:45,493] [INFO] Running command: blastn -query GCF_024171925.1_ASM2417192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c603fdd-3f8b-43a0-ba33-0c508050eb36/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171925.1_ASM2417192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:47,497] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:47,502] [INFO] Selected 16 target genomes.
[2024-01-24 11:14:47,503] [INFO] Target genome list was writen to GCF_024171925.1_ASM2417192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:47,510] [INFO] Task started: fastANI
[2024-01-24 11:14:47,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg22ab8f5f-e9b8-434b-8ceb-03df107d9411/GCF_024171925.1_ASM2417192v1_genomic.fna.gz --refList GCF_024171925.1_ASM2417192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171925.1_ASM2417192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:14,447] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:14,459] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:15:14,459] [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_016907695.1	s__Actinokineospora baliensis	89.9715	2156	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	86.8357	1920	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_000482865.1	s__Actinokineospora inagensis	84.1422	1595	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	82.9987	1578	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	82.7499	1458	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	81.8425	1155	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362515.1	s__Actinokineospora alba	81.1092	1094	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001940455.1	s__Actinokineospora bangkokensis	80.8587	1223	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	80.6217	1164	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023245.1	s__Actinosynnema mirum	78.5103	977	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	99.51	99.51	0.95	0.95	3	-
GCF_002354875.1	s__Actinosynnema auranticum	78.4424	1002	2689	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCA_903862935.1	s__Palsa-1447 sp903862935	74.9945	53	2689	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.95	99.89	0.98	0.97	5	-
GCA_002420005.1	s__UBA5704 sp002420005	74.8499	260	2689	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178945.1	s__JADJWL01 sp016178945	74.6416	125	2689	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADJWL01	95.0	98.66	98.66	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:14,461] [INFO] GTDB search result was written to GCF_024171925.1_ASM2417192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:14,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:14,465] [INFO] DFAST_QC result json was written to GCF_024171925.1_ASM2417192v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:14,466] [INFO] DFAST_QC completed!
[2024-01-24 11:15:14,466] [INFO] Total running time: 0h2m48s