[2024-01-24 12:31:51,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,255] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,255] [INFO] DQC Reference Directory: /var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference
[2024-01-24 12:31:52,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,513] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bca2383-4dc8-4bc1-8f53-69a3a9083c53/GCF_000334455.1_ASM33445v1_genomic.fna.gz | prodigal -d GCF_000334455.1_ASM33445v1_genomic.fna/cds.fna -a GCF_000334455.1_ASM33445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:09,714] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:09,714] [INFO] Task started: HMMsearch
[2024-01-24 12:32:09,714] [INFO] Running command: hmmsearch --tblout GCF_000334455.1_ASM33445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference/reference_markers.hmm GCF_000334455.1_ASM33445v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:10,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:10,017] [INFO] Found 6/6 markers.
[2024-01-24 12:32:10,066] [INFO] Query marker FASTA was written to GCF_000334455.1_ASM33445v1_genomic.fna/markers.fasta
[2024-01-24 12:32:10,067] [INFO] Task started: Blastn
[2024-01-24 12:32:10,067] [INFO] Running command: blastn -query GCF_000334455.1_ASM33445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference/reference_markers.fasta -out GCF_000334455.1_ASM33445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:11,269] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:11,275] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:11,275] [INFO] Target genome list was writen to GCF_000334455.1_ASM33445v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:11,283] [INFO] Task started: fastANI
[2024-01-24 12:32:11,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bca2383-4dc8-4bc1-8f53-69a3a9083c53/GCF_000334455.1_ASM33445v1_genomic.fna.gz --refList GCF_000334455.1_ASM33445v1_genomic.fna/target_genomes.txt --output GCF_000334455.1_ASM33445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:28,567] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:28,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:28,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:28,581] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:28,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:28,581] [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 soli	strain=NBRC 108243	GCA_000334455.1	320799	320799	type	True	100.0	1760	1762	95	conclusive
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	79.9978	736	1762	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	79.939	762	1762	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.9303	762	1762	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	79.9131	728	1762	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	79.9097	738	1762	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	79.7932	846	1762	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	79.754	739	1762	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	79.7225	796	1762	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_000716975.1	2055	2055	suspected-type	True	79.7191	800	1762	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	79.7069	756	1762	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	79.6905	797	1762	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	79.6724	808	1762	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	79.5702	750	1762	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	79.4772	719	1762	95	below_threshold
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	78.6187	437	1762	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	78.6052	533	1762	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	78.5057	545	1762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:28,583] [INFO] DFAST Taxonomy check result was written to GCF_000334455.1_ASM33445v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:28,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:28,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:28,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference/checkm_data
[2024-01-24 12:32:28,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:28,637] [INFO] Task started: CheckM
[2024-01-24 12:32:28,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000334455.1_ASM33445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000334455.1_ASM33445v1_genomic.fna/checkm_input GCF_000334455.1_ASM33445v1_genomic.fna/checkm_result
[2024-01-24 12:33:32,085] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:32,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:32,112] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:32,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:32,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000334455.1_ASM33445v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:32,113] [INFO] Task started: Blastn
[2024-01-24 12:33:32,113] [INFO] Running command: blastn -query GCF_000334455.1_ASM33445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1187590-08ea-498d-b532-8aef63b30170/dqc_reference/reference_markers_gtdb.fasta -out GCF_000334455.1_ASM33445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:33,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:33,828] [INFO] Selected 17 target genomes.
[2024-01-24 12:33:33,828] [INFO] Target genome list was writen to GCF_000334455.1_ASM33445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:33,840] [INFO] Task started: fastANI
[2024-01-24 12:33:33,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bca2383-4dc8-4bc1-8f53-69a3a9083c53/GCF_000334455.1_ASM33445v1_genomic.fna.gz --refList GCF_000334455.1_ASM33445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000334455.1_ASM33445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:51,965] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:51,991] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:51,991] [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_000334455.1	s__Gordonia soli	100.0	1760	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000225505.1	s__Gordonia alkanivorans	80.0013	744	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.26	97.87	0.90	0.88	6	-
GCF_000327325.1	s__Gordonia rubripertincta	79.9876	737	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000298235.1	s__Gordonia namibiensis	79.9652	757	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_900105725.1	s__Gordonia westfalica	79.9391	814	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332995.1	s__Gordonia amicalis	79.898	730	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCF_003855095.1	s__Gordonia insulae	79.8211	842	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485495.1	s__Gordonia desulfuricans	79.7568	739	1762	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	79.7458	792	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	-
GCF_002149015.1	s__Gordonia lacunae	79.6496	803	1762	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	79.595	747	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002700145.1	s__Gordonia sp002700145	79.514	685	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009862785.1	s__Gordonia sp009862785	79.465	758	1762	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	79.4544	723	1762	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	79.3652	772	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241325.1	s__Gordonia polyisoprenivorans	79.2834	751	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.60	97.62	0.90	0.79	11	-
GCF_009932475.1	s__Gordonia spumicola	78.5979	534	1762	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:51,993] [INFO] GTDB search result was written to GCF_000334455.1_ASM33445v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:51,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:51,999] [INFO] DFAST_QC result json was written to GCF_000334455.1_ASM33445v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:51,999] [INFO] DFAST_QC completed!
[2024-01-24 12:33:52,000] [INFO] Total running time: 0h2m1s