[2024-01-25 19:31:51,378] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,380] [INFO] DQC Reference Directory: /var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference
[2024-01-25 19:31:52,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,507] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,507] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cc65c38-cd86-4e0d-a38f-16fe4a90cbd7/GCF_027620355.1_ASM2762035v1_genomic.fna.gz | prodigal -d GCF_027620355.1_ASM2762035v1_genomic.fna/cds.fna -a GCF_027620355.1_ASM2762035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:13,550] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:13,551] [INFO] Task started: HMMsearch
[2024-01-25 19:32:13,551] [INFO] Running command: hmmsearch --tblout GCF_027620355.1_ASM2762035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference/reference_markers.hmm GCF_027620355.1_ASM2762035v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:13,894] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:13,895] [INFO] Found 6/6 markers.
[2024-01-25 19:32:13,965] [INFO] Query marker FASTA was written to GCF_027620355.1_ASM2762035v1_genomic.fna/markers.fasta
[2024-01-25 19:32:13,965] [INFO] Task started: Blastn
[2024-01-25 19:32:13,965] [INFO] Running command: blastn -query GCF_027620355.1_ASM2762035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference/reference_markers.fasta -out GCF_027620355.1_ASM2762035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:15,265] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:15,268] [INFO] Selected 19 target genomes.
[2024-01-25 19:32:15,268] [INFO] Target genome list was writen to GCF_027620355.1_ASM2762035v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:15,274] [INFO] Task started: fastANI
[2024-01-25 19:32:15,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc65c38-cd86-4e0d-a38f-16fe4a90cbd7/GCF_027620355.1_ASM2762035v1_genomic.fna.gz --refList GCF_027620355.1_ASM2762035v1_genomic.fna/target_genomes.txt --output GCF_027620355.1_ASM2762035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:59,788] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:59,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:59,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:59,802] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:59,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:59,802] [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
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	98.2619	2594	2872	95	conclusive
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	84.8853	1855	2872	95	below_threshold
Nonomuraea glycinis	strain=CGMCC 4.7430	GCA_014646515.1	2047744	2047744	type	True	84.6276	1875	2872	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	84.6075	1874	2872	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	83.9062	1696	2872	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.902	1692	2872	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	83.6055	1842	2872	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.6007	1129	2872	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	83.598	1810	2872	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.4112	1618	2872	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	83.3752	1694	2872	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	83.2646	1723	2872	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.2083	1825	2872	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.0957	1722	2872	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	83.0781	1674	2872	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	82.9552	1699	2872	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	82.9237	1771	2872	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	82.8784	1639	2872	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.8566	1752	2872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:59,804] [INFO] DFAST Taxonomy check result was written to GCF_027620355.1_ASM2762035v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:59,804] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:59,804] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:59,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference/checkm_data
[2024-01-25 19:32:59,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:59,885] [INFO] Task started: CheckM
[2024-01-25 19:32:59,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027620355.1_ASM2762035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027620355.1_ASM2762035v1_genomic.fna/checkm_input GCF_027620355.1_ASM2762035v1_genomic.fna/checkm_result
[2024-01-25 19:34:18,013] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:18,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.21%
Strain heterogeneity: 28.57%
--------------------------------------------------------------------------------
[2024-01-25 19:34:18,044] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:18,044] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:18,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027620355.1_ASM2762035v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:18,046] [INFO] Task started: Blastn
[2024-01-25 19:34:18,046] [INFO] Running command: blastn -query GCF_027620355.1_ASM2762035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc387124a-b16a-49fd-89c3-ed01af5b4c56/dqc_reference/reference_markers_gtdb.fasta -out GCF_027620355.1_ASM2762035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:20,235] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:20,239] [INFO] Selected 18 target genomes.
[2024-01-25 19:34:20,239] [INFO] Target genome list was writen to GCF_027620355.1_ASM2762035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:20,249] [INFO] Task started: fastANI
[2024-01-25 19:34:20,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc65c38-cd86-4e0d-a38f-16fe4a90cbd7/GCF_027620355.1_ASM2762035v1_genomic.fna.gz --refList GCF_027620355.1_ASM2762035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027620355.1_ASM2762035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:04,370] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:04,381] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:04,382] [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_008017515.1	s__Nonomuraea sp008017515	98.6051	2702	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001083785.1	s__Nonomuraea sp001083785	85.2215	1840	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646515.1	s__Nonomuraea glycinis	84.6663	1866	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	83.8708	1703	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379885.1	s__Nonomuraea coxensis	83.6803	1793	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	83.3966	1623	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	83.3274	1701	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	83.3208	1710	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_006334985.2	s__Nonomuraea phyllanthi	83.2389	1810	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	83.1672	1686	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348995.1	s__Nonomuraea terrae	83.1448	1604	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	82.9259	1806	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	82.9214	1707	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	82.9124	1773	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	82.8752	1643	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_900108335.1	s__Nonomuraea solani	82.7885	1875	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	82.6672	1771	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_002093975.1	s__Nonomuraea rubra_A	81.5792	1457	2872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:04,385] [INFO] GTDB search result was written to GCF_027620355.1_ASM2762035v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:04,385] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:04,390] [INFO] DFAST_QC result json was written to GCF_027620355.1_ASM2762035v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:04,390] [INFO] DFAST_QC completed!
[2024-01-25 19:35:04,390] [INFO] Total running time: 0h3m13s