[2024-01-24 14:47:08,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference
[2024-01-24 14:47:09,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,578] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg15d01e98-16d4-479f-a78c-12269f13536f/GCF_002934265.1_ASM293426v1_genomic.fna.gz | prodigal -d GCF_002934265.1_ASM293426v1_genomic.fna/cds.fna -a GCF_002934265.1_ASM293426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:38,582] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:38,582] [INFO] Task started: HMMsearch
[2024-01-24 14:47:38,583] [INFO] Running command: hmmsearch --tblout GCF_002934265.1_ASM293426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference/reference_markers.hmm GCF_002934265.1_ASM293426v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:39,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:39,027] [INFO] Found 6/6 markers.
[2024-01-24 14:47:39,115] [INFO] Query marker FASTA was written to GCF_002934265.1_ASM293426v1_genomic.fna/markers.fasta
[2024-01-24 14:47:39,116] [INFO] Task started: Blastn
[2024-01-24 14:47:39,116] [INFO] Running command: blastn -query GCF_002934265.1_ASM293426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference/reference_markers.fasta -out GCF_002934265.1_ASM293426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:40,618] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:40,625] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:40,626] [INFO] Target genome list was writen to GCF_002934265.1_ASM293426v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:40,631] [INFO] Task started: fastANI
[2024-01-24 14:47:40,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg15d01e98-16d4-479f-a78c-12269f13536f/GCF_002934265.1_ASM293426v1_genomic.fna.gz --refList GCF_002934265.1_ASM293426v1_genomic.fna/target_genomes.txt --output GCF_002934265.1_ASM293426v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:10,446] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:10,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:10,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:10,463] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:10,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:10,464] [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 auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	100.0	2777	2780	95	conclusive
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	83.5839	1607	2780	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	83.2631	1567	2780	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	83.2551	1533	2780	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	83.2506	1593	2780	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	83.0747	1565	2780	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	83.0738	1518	2780	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	82.849	1446	2780	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	81.9549	1199	2780	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.4564	904	2780	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.2935	867	2780	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	78.2505	1069	2780	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	78.0113	1002	2780	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.7699	643	2780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:10,467] [INFO] DFAST Taxonomy check result was written to GCF_002934265.1_ASM293426v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:10,467] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:10,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:10,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference/checkm_data
[2024-01-24 14:48:10,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:10,545] [INFO] Task started: CheckM
[2024-01-24 14:48:10,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934265.1_ASM293426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934265.1_ASM293426v1_genomic.fna/checkm_input GCF_002934265.1_ASM293426v1_genomic.fna/checkm_result
[2024-01-24 14:49:47,441] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:47,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:47,469] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:47,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:47,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934265.1_ASM293426v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:47,471] [INFO] Task started: Blastn
[2024-01-24 14:49:47,471] [INFO] Running command: blastn -query GCF_002934265.1_ASM293426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg993a40fd-7897-45a2-8e0e-25359a68641d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934265.1_ASM293426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:49,884] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:49,887] [INFO] Selected 12 target genomes.
[2024-01-24 14:49:49,887] [INFO] Target genome list was writen to GCF_002934265.1_ASM293426v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:49,904] [INFO] Task started: fastANI
[2024-01-24 14:49:49,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg15d01e98-16d4-479f-a78c-12269f13536f/GCF_002934265.1_ASM293426v1_genomic.fna.gz --refList GCF_002934265.1_ASM293426v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934265.1_ASM293426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:18,936] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:18,948] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:18,948] [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_002934265.1	s__Actinokineospora auranticolor	100.0	2777	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374445.1	s__Actinokineospora enzanensis	83.6347	1599	2780	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	83.2361	1573	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_016907695.1	s__Actinokineospora baliensis	83.0655	1520	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	82.8256	1450	2780	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	81.9539	1199	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	81.3727	1299	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_009745975.1	s__Actinokineospora pegani	81.0859	1154	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	80.9477	1297	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323725.1	s__Actinokineospora xionganensis	80.8629	1103	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	78.747	932	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354875.1	s__Actinosynnema auranticum	78.5898	1100	2780	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:18,951] [INFO] GTDB search result was written to GCF_002934265.1_ASM293426v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:18,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:18,955] [INFO] DFAST_QC result json was written to GCF_002934265.1_ASM293426v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:18,956] [INFO] DFAST_QC completed!
[2024-01-24 14:50:18,956] [INFO] Total running time: 0h3m11s