[2024-01-24 12:29:33,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:34,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:34,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference
[2024-01-24 12:29:35,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:35,218] [INFO] Task started: Prodigal
[2024-01-24 12:29:35,218] [INFO] Running command: gunzip -c /var/lib/cwl/stg74b93aa4-87a5-4e69-b3e6-4d2f5c106e25/GCF_024734075.1_ASM2473407v1_genomic.fna.gz | prodigal -d GCF_024734075.1_ASM2473407v1_genomic.fna/cds.fna -a GCF_024734075.1_ASM2473407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:54,240] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:54,240] [INFO] Task started: HMMsearch
[2024-01-24 12:29:54,241] [INFO] Running command: hmmsearch --tblout GCF_024734075.1_ASM2473407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference/reference_markers.hmm GCF_024734075.1_ASM2473407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:54,528] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:54,530] [INFO] Found 6/6 markers.
[2024-01-24 12:29:54,572] [INFO] Query marker FASTA was written to GCF_024734075.1_ASM2473407v1_genomic.fna/markers.fasta
[2024-01-24 12:29:54,572] [INFO] Task started: Blastn
[2024-01-24 12:29:54,573] [INFO] Running command: blastn -query GCF_024734075.1_ASM2473407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference/reference_markers.fasta -out GCF_024734075.1_ASM2473407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:55,671] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:55,675] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:55,675] [INFO] Target genome list was writen to GCF_024734075.1_ASM2473407v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:55,694] [INFO] Task started: fastANI
[2024-01-24 12:29:55,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b93aa4-87a5-4e69-b3e6-4d2f5c106e25/GCF_024734075.1_ASM2473407v1_genomic.fna.gz --refList GCF_024734075.1_ASM2473407v1_genomic.fna/target_genomes.txt --output GCF_024734075.1_ASM2473407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:10,725] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:10,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:10,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:10,748] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:10,749] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:10,749] [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 mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	100.0	1794	1796	95	conclusive
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	99.9901	1781	1796	95	conclusive
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	81.2352	1034	1796	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	81.1682	1006	1796	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	80.57	955	1796	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	80.2043	824	1796	95	below_threshold
Gordonia westfalica	strain=DSM 44215	GCA_900105725.1	158898	158898	type	True	80.1922	818	1796	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	80.1764	813	1796	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	80.0468	783	1796	95	below_threshold
Gordonia amicalis	strain=NBRC 100051	GCA_000332995.1	89053	89053	type	True	80.0091	780	1796	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	79.7457	776	1796	95	below_threshold
Gordonia sihwensis	strain=NBRC 108236	GCA_000333035.1	173559	173559	type	True	78.7479	475	1796	95	below_threshold
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	78.4676	460	1796	95	below_threshold
Nocardia brasiliensis	strain=NBRC 14402	GCA_000308475.2	37326	37326	suspected-type	True	77.5766	422	1796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:10,751] [INFO] DFAST Taxonomy check result was written to GCF_024734075.1_ASM2473407v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:10,752] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:10,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:10,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference/checkm_data
[2024-01-24 12:30:10,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:10,804] [INFO] Task started: CheckM
[2024-01-24 12:30:10,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024734075.1_ASM2473407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024734075.1_ASM2473407v1_genomic.fna/checkm_input GCF_024734075.1_ASM2473407v1_genomic.fna/checkm_result
[2024-01-24 12:31:40,782] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:40,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:40,810] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:40,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:40,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024734075.1_ASM2473407v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:40,811] [INFO] Task started: Blastn
[2024-01-24 12:31:40,811] [INFO] Running command: blastn -query GCF_024734075.1_ASM2473407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62d42ea3-05de-459c-a580-fd785cc9ed0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_024734075.1_ASM2473407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:42,417] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:42,421] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:42,421] [INFO] Target genome list was writen to GCF_024734075.1_ASM2473407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:42,479] [INFO] Task started: fastANI
[2024-01-24 12:31:42,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b93aa4-87a5-4e69-b3e6-4d2f5c106e25/GCF_024734075.1_ASM2473407v1_genomic.fna.gz --refList GCF_024734075.1_ASM2473407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024734075.1_ASM2473407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:55,643] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:55,653] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:55,653] [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_009828195.1	s__Gordonia sp009828195	99.9901	1781	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002700145.1	s__Gordonia sp002700145	86.5655	1242	1796	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	81.5917	1082	1796	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	81.2243	1036	1796	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	81.1753	1005	1796	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	81.1706	1028	1796	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	80.1773	814	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000327325.1	s__Gordonia rubripertincta	80.1752	758	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000332995.1	s__Gordonia amicalis	80.0196	779	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.45	97.39	0.94	0.91	7	-
GCA_013348785.1	s__Gordonia sp013348785	79.1312	493	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333035.1	s__Gordonia sihwensis	78.7656	473	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	-
GCF_000423025.1	s__Gordonia shandongensis	78.4673	460	1796	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 12:31:55,655] [INFO] GTDB search result was written to GCF_024734075.1_ASM2473407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:55,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:55,660] [INFO] DFAST_QC result json was written to GCF_024734075.1_ASM2473407v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:55,661] [INFO] DFAST_QC completed!
[2024-01-24 12:31:55,661] [INFO] Total running time: 0h2m22s