[2024-01-24 13:47:10,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference
[2024-01-24 13:47:12,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:12,023] [INFO] Task started: Prodigal
[2024-01-24 13:47:12,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg314137fe-3543-4dcb-8ed2-bddeaee1627c/GCF_020731255.1_ASM2073125v1_genomic.fna.gz | prodigal -d GCF_020731255.1_ASM2073125v1_genomic.fna/cds.fna -a GCF_020731255.1_ASM2073125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:35,435] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:35,436] [INFO] Task started: HMMsearch
[2024-01-24 13:47:35,436] [INFO] Running command: hmmsearch --tblout GCF_020731255.1_ASM2073125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference/reference_markers.hmm GCF_020731255.1_ASM2073125v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:35,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:35,797] [INFO] Found 6/6 markers.
[2024-01-24 13:47:35,848] [INFO] Query marker FASTA was written to GCF_020731255.1_ASM2073125v1_genomic.fna/markers.fasta
[2024-01-24 13:47:35,848] [INFO] Task started: Blastn
[2024-01-24 13:47:35,848] [INFO] Running command: blastn -query GCF_020731255.1_ASM2073125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference/reference_markers.fasta -out GCF_020731255.1_ASM2073125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:37,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:37,122] [INFO] Selected 14 target genomes.
[2024-01-24 13:47:37,122] [INFO] Target genome list was writen to GCF_020731255.1_ASM2073125v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:37,164] [INFO] Task started: fastANI
[2024-01-24 13:47:37,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg314137fe-3543-4dcb-8ed2-bddeaee1627c/GCF_020731255.1_ASM2073125v1_genomic.fna.gz --refList GCF_020731255.1_ASM2073125v1_genomic.fna/target_genomes.txt --output GCF_020731255.1_ASM2073125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:53,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:53,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:53,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:53,676] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:47:53,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:53,677] [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
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	100.0	1760	1760	95	conclusive
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	99.9988	1758	1760	95	conclusive
Gordonia bronchialis	strain=DSM 43247	GCA_000024785.1	2054	2054	type	True	99.9988	1756	1760	95	conclusive
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	80.8811	893	1760	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	80.7767	916	1760	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	80.6648	880	1760	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	80.6185	888	1760	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	80.4706	875	1760	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	80.4397	856	1760	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	80.0141	911	1760	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	80.0079	809	1760	95	below_threshold
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	79.684	746	1760	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	79.5221	837	1760	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	79.3337	679	1760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:53,685] [INFO] DFAST Taxonomy check result was written to GCF_020731255.1_ASM2073125v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:53,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:53,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:53,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference/checkm_data
[2024-01-24 13:47:53,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:53,753] [INFO] Task started: CheckM
[2024-01-24 13:47:53,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020731255.1_ASM2073125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020731255.1_ASM2073125v1_genomic.fna/checkm_input GCF_020731255.1_ASM2073125v1_genomic.fna/checkm_result
[2024-01-24 13:49:13,225] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:13,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:13,251] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:13,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:13,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020731255.1_ASM2073125v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:13,253] [INFO] Task started: Blastn
[2024-01-24 13:49:13,253] [INFO] Running command: blastn -query GCF_020731255.1_ASM2073125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa05e42f-8f98-440d-9dd9-8782889c4544/dqc_reference/reference_markers_gtdb.fasta -out GCF_020731255.1_ASM2073125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,224] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,228] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:15,229] [INFO] Target genome list was writen to GCF_020731255.1_ASM2073125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:15,245] [INFO] Task started: fastANI
[2024-01-24 13:49:15,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg314137fe-3543-4dcb-8ed2-bddeaee1627c/GCF_020731255.1_ASM2073125v1_genomic.fna.gz --refList GCF_020731255.1_ASM2073125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020731255.1_ASM2073125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:36,195] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:36,215] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:36,216] [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_000024785.1	s__Gordonia bronchialis	99.9988	1756	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_900105725.1	s__Gordonia westfalica	80.9324	963	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327325.1	s__Gordonia rubripertincta	80.8845	893	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_011290605.1	s__Gordonia sp002009645	80.6944	911	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCF_000298235.1	s__Gordonia namibiensis	80.6729	878	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000332995.1	s__Gordonia amicalis	80.6652	879	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_001485495.1	s__Gordonia desulfuricans	80.4534	854	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_001698225.1	s__Gordonia terrae	80.3716	902	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCA_002700145.1	s__Gordonia sp002700145	80.2211	806	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	80.1295	879	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	80.0587	907	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828195.1	s__Gordonia sp009828195	80.008	810	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797825.1	s__Gordonia sp003797825	79.9499	900	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241345.1	s__Gordonia amarae	79.674	747	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
GCF_009862785.1	s__Gordonia sp009862785	79.54	805	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673215.1	s__Gordonia hankookensis	79.528	836	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
GCF_003797185.1	s__Gordonia oryzae	79.5224	737	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009914535.1	s__Gordonia pseudoamarae	79.301	693	1760	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.95	99.95	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:36,217] [INFO] GTDB search result was written to GCF_020731255.1_ASM2073125v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:36,218] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:36,225] [INFO] DFAST_QC result json was written to GCF_020731255.1_ASM2073125v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:36,226] [INFO] DFAST_QC completed!
[2024-01-24 13:49:36,226] [INFO] Total running time: 0h2m25s