[2024-01-24 11:35:23,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference
[2024-01-24 11:35:26,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg27ddc3eb-85bf-4289-9535-90e4d26a68da/GCF_023656545.1_ASM2365654v1_genomic.fna.gz | prodigal -d GCF_023656545.1_ASM2365654v1_genomic.fna/cds.fna -a GCF_023656545.1_ASM2365654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:41,376] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:41,376] [INFO] Task started: HMMsearch
[2024-01-24 11:35:41,376] [INFO] Running command: hmmsearch --tblout GCF_023656545.1_ASM2365654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference/reference_markers.hmm GCF_023656545.1_ASM2365654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:41,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:41,761] [INFO] Found 6/6 markers.
[2024-01-24 11:35:41,817] [INFO] Query marker FASTA was written to GCF_023656545.1_ASM2365654v1_genomic.fna/markers.fasta
[2024-01-24 11:35:41,817] [INFO] Task started: Blastn
[2024-01-24 11:35:41,817] [INFO] Running command: blastn -query GCF_023656545.1_ASM2365654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference/reference_markers.fasta -out GCF_023656545.1_ASM2365654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:43,047] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:43,051] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:43,051] [INFO] Target genome list was writen to GCF_023656545.1_ASM2365654v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:43,057] [INFO] Task started: fastANI
[2024-01-24 11:35:43,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ddc3eb-85bf-4289-9535-90e4d26a68da/GCF_023656545.1_ASM2365654v1_genomic.fna.gz --refList GCF_023656545.1_ASM2365654v1_genomic.fna/target_genomes.txt --output GCF_023656545.1_ASM2365654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:11,180] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:11,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:11,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:11,195] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:11,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:11,196] [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
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	100.0	1751	1767	95	conclusive
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	88.2786	1194	1767	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	88.0164	1190	1767	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	87.4168	1292	1767	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	87.276	1263	1767	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	86.8664	1279	1767	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	86.7526	1208	1767	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	86.7146	1160	1767	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	86.6751	1250	1767	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	86.2451	1101	1767	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	86.0	1117	1767	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	85.9311	1195	1767	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	85.2112	1115	1767	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	85.1502	1031	1767	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.1203	1062	1767	95	below_threshold
Micromonospora musae	strain=MS1-9	GCA_003626635.1	1894970	1894970	type	True	84.8962	1132	1767	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.7957	1040	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:11,197] [INFO] DFAST Taxonomy check result was written to GCF_023656545.1_ASM2365654v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:11,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:11,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:11,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference/checkm_data
[2024-01-24 11:36:11,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:11,257] [INFO] Task started: CheckM
[2024-01-24 11:36:11,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023656545.1_ASM2365654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023656545.1_ASM2365654v1_genomic.fna/checkm_input GCF_023656545.1_ASM2365654v1_genomic.fna/checkm_result
[2024-01-24 11:36:57,260] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:57,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:57,286] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:57,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:57,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023656545.1_ASM2365654v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:57,287] [INFO] Task started: Blastn
[2024-01-24 11:36:57,287] [INFO] Running command: blastn -query GCF_023656545.1_ASM2365654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd02a78ee-7b49-497a-9eb7-044169bdd548/dqc_reference/reference_markers_gtdb.fasta -out GCF_023656545.1_ASM2365654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:59,138] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:59,143] [INFO] Selected 23 target genomes.
[2024-01-24 11:36:59,143] [INFO] Target genome list was writen to GCF_023656545.1_ASM2365654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:59,192] [INFO] Task started: fastANI
[2024-01-24 11:36:59,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg27ddc3eb-85bf-4289-9535-90e4d26a68da/GCF_023656545.1_ASM2365654v1_genomic.fna.gz --refList GCF_023656545.1_ASM2365654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023656545.1_ASM2365654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:34,332] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:34,353] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:37:34,354] [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_900090315.1	s__Micromonospora citrea	88.3214	1190	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345505.1	s__Micromonospora sp004345505	88.0704	1187	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.85	96.85	0.87	0.87	2	-
GCF_900091445.1	s__Micromonospora echinofusca	88.0127	1190	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_003236335.1	s__Micromonospora deserti	87.9951	1043	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091625.1	s__Micromonospora peucetia	87.9794	1183	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	87.9045	1125	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	87.2657	1264	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_004217615.1	s__Micromonospora kangleipakensis	86.8437	1281	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	86.7377	1157	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	86.6946	1189	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_016598485.1	s__Micromonospora veneta	86.6759	1249	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090285.1	s__Micromonospora inositola	86.6731	1218	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	86.5061	1114	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070045.1	s__Micromonospora sp018070045	86.3975	1261	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707425.1	s__Micromonospora sp009707425	86.2934	1180	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	86.2125	1044	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900091555.1	s__Micromonospora mirobrigensis	86.034	1114	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	85.9823	1120	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	85.9277	1196	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_008868155.1	s__Micromonospora sp008868155	85.6633	1050	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297395.2	s__Micromonospora lupini	85.6039	1137	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803395.1	s__Micromonospora sp016803395	85.3722	1034	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626635.1	s__Micromonospora musae	84.8967	1132	1767	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.26	97.34	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:34,355] [INFO] GTDB search result was written to GCF_023656545.1_ASM2365654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:34,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:34,364] [INFO] DFAST_QC result json was written to GCF_023656545.1_ASM2365654v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:34,364] [INFO] DFAST_QC completed!
[2024-01-24 11:37:34,364] [INFO] Total running time: 0h2m11s