[2024-01-24 13:46:25,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference
[2024-01-24 13:46:27,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,058] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,058] [INFO] Running command: gunzip -c /var/lib/cwl/stgd067806d-761b-4660-8e92-a10cad6f9d61/GCF_014673215.1_ASM1467321v1_genomic.fna.gz | prodigal -d GCF_014673215.1_ASM1467321v1_genomic.fna/cds.fna -a GCF_014673215.1_ASM1467321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:47,569] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:47,570] [INFO] Task started: HMMsearch
[2024-01-24 13:46:47,570] [INFO] Running command: hmmsearch --tblout GCF_014673215.1_ASM1467321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference/reference_markers.hmm GCF_014673215.1_ASM1467321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:47,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:47,897] [INFO] Found 6/6 markers.
[2024-01-24 13:46:47,943] [INFO] Query marker FASTA was written to GCF_014673215.1_ASM1467321v1_genomic.fna/markers.fasta
[2024-01-24 13:46:47,944] [INFO] Task started: Blastn
[2024-01-24 13:46:47,944] [INFO] Running command: blastn -query GCF_014673215.1_ASM1467321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference/reference_markers.fasta -out GCF_014673215.1_ASM1467321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:49,136] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:49,139] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:49,139] [INFO] Target genome list was writen to GCF_014673215.1_ASM1467321v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:49,146] [INFO] Task started: fastANI
[2024-01-24 13:46:49,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgd067806d-761b-4660-8e92-a10cad6f9d61/GCF_014673215.1_ASM1467321v1_genomic.fna.gz --refList GCF_014673215.1_ASM1467321v1_genomic.fna/target_genomes.txt --output GCF_014673215.1_ASM1467321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:07,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:07,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:07,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:07,151] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:07,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:07,152] [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 hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	100.0	1737	1737	95	conclusive
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	82.4682	1256	1737	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	80.6505	951	1737	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	80.6301	958	1737	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	80.467	933	1737	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.7868	761	1737	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	79.724	756	1737	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	79.7106	819	1737	95	below_threshold
Gordonia bronchialis	strain=DSM 43247	GCA_000024785.1	2054	2054	type	True	79.6893	820	1737	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	79.679	815	1737	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	79.6594	749	1737	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	79.6502	752	1737	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	79.6045	767	1737	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	79.5885	799	1737	95	below_threshold
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	79.1128	654	1737	95	below_threshold
Gordonia otitidis	strain=NBRC 100426	GCA_000248075.2	249058	249058	type	True	79.0053	617	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:07,153] [INFO] DFAST Taxonomy check result was written to GCF_014673215.1_ASM1467321v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:07,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:07,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:07,154] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference/checkm_data
[2024-01-24 13:47:07,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:07,203] [INFO] Task started: CheckM
[2024-01-24 13:47:07,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014673215.1_ASM1467321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014673215.1_ASM1467321v1_genomic.fna/checkm_input GCF_014673215.1_ASM1467321v1_genomic.fna/checkm_result
[2024-01-24 13:48:19,665] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:19,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:19,687] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:19,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:19,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014673215.1_ASM1467321v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:19,689] [INFO] Task started: Blastn
[2024-01-24 13:48:19,689] [INFO] Running command: blastn -query GCF_014673215.1_ASM1467321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg301c217c-8785-4739-9782-d6c4a586ac18/dqc_reference/reference_markers_gtdb.fasta -out GCF_014673215.1_ASM1467321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:21,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:21,296] [INFO] Selected 12 target genomes.
[2024-01-24 13:48:21,296] [INFO] Target genome list was writen to GCF_014673215.1_ASM1467321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:21,324] [INFO] Task started: fastANI
[2024-01-24 13:48:21,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgd067806d-761b-4660-8e92-a10cad6f9d61/GCF_014673215.1_ASM1467321v1_genomic.fna.gz --refList GCF_014673215.1_ASM1467321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014673215.1_ASM1467321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:35,935] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:35,955] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:35,955] [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_014673215.1	s__Gordonia hankookensis	100.0	1737	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	conclusive
GCF_009862785.1	s__Gordonia sp009862785	85.9987	1383	1737	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	82.4381	1261	1737	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	81.3986	1140	1737	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	80.6366	957	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700145.1	s__Gordonia sp002700145	80.603	911	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298195.1	s__Gordonia rhizosphera	80.4733	932	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193205.1	s__Gordonia sediminis	80.4445	973	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024785.1	s__Gordonia bronchialis	79.6946	819	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000332995.1	s__Gordonia amicalis	79.6545	748	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_900105725.1	s__Gordonia westfalica	79.5764	800	1737	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	79.1057	655	1737	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:35,962] [INFO] GTDB search result was written to GCF_014673215.1_ASM1467321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:35,963] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:35,968] [INFO] DFAST_QC result json was written to GCF_014673215.1_ASM1467321v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:35,969] [INFO] DFAST_QC completed!
[2024-01-24 13:48:35,969] [INFO] Total running time: 0h2m10s