[2024-01-24 14:06:06,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference
[2024-01-24 14:06:07,460] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,461] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,461] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ffd609-6b79-4afb-a679-0d3fac205e76/GCF_002263495.1_ASM226349v1_genomic.fna.gz | prodigal -d GCF_002263495.1_ASM226349v1_genomic.fna/cds.fna -a GCF_002263495.1_ASM226349v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:28,872] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:28,872] [INFO] Task started: HMMsearch
[2024-01-24 14:06:28,872] [INFO] Running command: hmmsearch --tblout GCF_002263495.1_ASM226349v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference/reference_markers.hmm GCF_002263495.1_ASM226349v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:29,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:29,236] [INFO] Found 6/6 markers.
[2024-01-24 14:06:29,283] [INFO] Query marker FASTA was written to GCF_002263495.1_ASM226349v1_genomic.fna/markers.fasta
[2024-01-24 14:06:29,283] [INFO] Task started: Blastn
[2024-01-24 14:06:29,283] [INFO] Running command: blastn -query GCF_002263495.1_ASM226349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference/reference_markers.fasta -out GCF_002263495.1_ASM226349v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:30,795] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:30,800] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:30,801] [INFO] Target genome list was writen to GCF_002263495.1_ASM226349v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:30,819] [INFO] Task started: fastANI
[2024-01-24 14:06:30,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ffd609-6b79-4afb-a679-0d3fac205e76/GCF_002263495.1_ASM226349v1_genomic.fna.gz --refList GCF_002263495.1_ASM226349v1_genomic.fna/target_genomes.txt --output GCF_002263495.1_ASM226349v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:55,745] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:55,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:55,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:55,767] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:55,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:55,768] [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
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	100.0	2047	2047	95	conclusive
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	99.7985	1776	2047	95	conclusive
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	86.9655	1514	2047	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	81.0533	1017	2047	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	81.0055	1062	2047	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	80.9706	956	2047	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.7557	898	2047	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	80.2465	712	2047	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	80.1909	747	2047	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	80.1827	849	2047	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	80.0984	809	2047	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.082	823	2047	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.9774	800	2047	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	79.9631	851	2047	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	79.784	670	2047	95	below_threshold
Nocardiopsis alba	strain=DSM 43377	GCA_000341225.1	53437	53437	type	True	79.5363	684	2047	95	below_threshold
Nocardiopsis xinjiangensis	strain=YIM 90004	GCA_000341145.1	124285	124285	type	True	79.141	636	2047	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	77.4298	515	2047	95	below_threshold
Corynebacterium pacaense	strain=Marseille-P2417	GCA_900169525.1	1816684	1816684	type	True	77.0967	88	2047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:55,770] [INFO] DFAST Taxonomy check result was written to GCF_002263495.1_ASM226349v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:55,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:55,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:55,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference/checkm_data
[2024-01-24 14:06:55,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:55,838] [INFO] Task started: CheckM
[2024-01-24 14:06:55,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002263495.1_ASM226349v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002263495.1_ASM226349v1_genomic.fna/checkm_input GCF_002263495.1_ASM226349v1_genomic.fna/checkm_result
[2024-01-24 14:08:03,406] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:03,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:03,434] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:03,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:03,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002263495.1_ASM226349v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:03,436] [INFO] Task started: Blastn
[2024-01-24 14:08:03,436] [INFO] Running command: blastn -query GCF_002263495.1_ASM226349v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c2b4d10-68cd-4862-a4b7-0335c725d6ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_002263495.1_ASM226349v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:05,458] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:05,462] [INFO] Selected 19 target genomes.
[2024-01-24 14:08:05,463] [INFO] Target genome list was writen to GCF_002263495.1_ASM226349v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:05,482] [INFO] Task started: fastANI
[2024-01-24 14:08:05,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ffd609-6b79-4afb-a679-0d3fac205e76/GCF_002263495.1_ASM226349v1_genomic.fna.gz --refList GCF_002263495.1_ASM226349v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002263495.1_ASM226349v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:30,119] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:30,140] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:30,141] [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_002263495.1	s__Nocardiopsis_C gilva	100.0	2047	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_014201195.1	s__Nocardiopsis_C mwathae	86.9728	1513	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	81.5448	1009	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	81.4964	952	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	81.4296	975	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_009728995.1	s__Streptomonospora sp009728995	81.1253	920	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	81.039	1056	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341105.1	s__Nocardiopsis_A potens	81.021	1021	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981225.1	s__Allosalinactinospora lopnorensis	81.0079	876	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allosalinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	80.6358	830	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_004363075.1	s__Actinorugispora endophytica	80.63	814	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	80.288	800	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_003014485.1	s__Murinocardiopsis flavida	79.8869	896	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Murinocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	79.7759	673	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018388625.1	s__Nocardiopsis sp018388625	79.6201	766	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341225.1	s__Nocardiopsis alba	79.5291	685	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	98.86	98.56	0.95	0.95	4	-
GCF_000341145.1	s__Nocardiopsis xinjiangensis	79.1491	635	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138725.1	s__Kutzneria viridogrisea	76.6556	502	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_016863255.1	s__Planosporangium mesophilum	76.5586	347	2047	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:30,143] [INFO] GTDB search result was written to GCF_002263495.1_ASM226349v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:30,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:30,148] [INFO] DFAST_QC result json was written to GCF_002263495.1_ASM226349v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:30,148] [INFO] DFAST_QC completed!
[2024-01-24 14:08:30,148] [INFO] Total running time: 0h2m24s