[2024-01-24 13:45:45,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference
[2024-01-24 13:45:47,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,133] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg90448218-382b-4f3f-a486-5f595da25308/GCF_011764565.1_ASM1176456v1_genomic.fna.gz | prodigal -d GCF_011764565.1_ASM1176456v1_genomic.fna/cds.fna -a GCF_011764565.1_ASM1176456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:20,475] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:20,476] [INFO] Task started: HMMsearch
[2024-01-24 13:46:20,476] [INFO] Running command: hmmsearch --tblout GCF_011764565.1_ASM1176456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference/reference_markers.hmm GCF_011764565.1_ASM1176456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:20,908] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:20,909] [INFO] Found 6/6 markers.
[2024-01-24 13:46:20,988] [INFO] Query marker FASTA was written to GCF_011764565.1_ASM1176456v1_genomic.fna/markers.fasta
[2024-01-24 13:46:20,989] [INFO] Task started: Blastn
[2024-01-24 13:46:20,989] [INFO] Running command: blastn -query GCF_011764565.1_ASM1176456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference/reference_markers.fasta -out GCF_011764565.1_ASM1176456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:22,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:22,203] [INFO] Selected 23 target genomes.
[2024-01-24 13:46:22,204] [INFO] Target genome list was writen to GCF_011764565.1_ASM1176456v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:22,265] [INFO] Task started: fastANI
[2024-01-24 13:46:22,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg90448218-382b-4f3f-a486-5f595da25308/GCF_011764565.1_ASM1176456v1_genomic.fna.gz --refList GCF_011764565.1_ASM1176456v1_genomic.fna/target_genomes.txt --output GCF_011764565.1_ASM1176456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:14,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:14,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:14,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:14,079] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:14,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:14,080] [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
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	100.0	3382	3382	95	conclusive
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	88.3382	2106	3382	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	87.7912	2238	3382	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	82.9749	1806	3382	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	80.2061	1065	3382	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.9742	915	3382	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	79.8668	1206	3382	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	79.8546	959	3382	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	79.7938	1252	3382	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	79.7221	1255	3382	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.6768	1112	3382	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.6449	1322	3382	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	79.591	1196	3382	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	79.5904	1326	3382	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	79.5747	1201	3382	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	79.5334	1202	3382	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	79.4023	1126	3382	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	79.3953	1176	3382	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	79.3864	1063	3382	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	79.3811	1128	3382	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	79.17	1335	3382	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	78.3055	1307	3382	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.3616	779	3382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,088] [INFO] DFAST Taxonomy check result was written to GCF_011764565.1_ASM1176456v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:14,089] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:14,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:14,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference/checkm_data
[2024-01-24 13:47:14,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:14,190] [INFO] Task started: CheckM
[2024-01-24 13:47:14,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011764565.1_ASM1176456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011764565.1_ASM1176456v1_genomic.fna/checkm_input GCF_011764565.1_ASM1176456v1_genomic.fna/checkm_result
[2024-01-24 13:49:32,459] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:32,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,487] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:32,488] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:32,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011764565.1_ASM1176456v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:32,488] [INFO] Task started: Blastn
[2024-01-24 13:49:32,489] [INFO] Running command: blastn -query GCF_011764565.1_ASM1176456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg994b82bc-0e08-4721-a022-fd91f617611a/dqc_reference/reference_markers_gtdb.fasta -out GCF_011764565.1_ASM1176456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:34,488] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:34,491] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:34,492] [INFO] Target genome list was writen to GCF_011764565.1_ASM1176456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:34,507] [INFO] Task started: fastANI
[2024-01-24 13:49:34,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg90448218-382b-4f3f-a486-5f595da25308/GCF_011764565.1_ASM1176456v1_genomic.fna.gz --refList GCF_011764565.1_ASM1176456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011764565.1_ASM1176456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:21,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:21,235] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:21,236] [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_011764565.1	s__Phytohabitans suffuscus	100.0	3382	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011764545.1	s__Phytohabitans flavus	88.232	2120	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	87.7892	2240	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	82.9722	1810	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	79.8923	954	3382	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	79.8735	1204	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_014648395.1	s__Micromonospora fulviviridis	79.7735	1257	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_006228125.1	s__Micromonospora orduensis	79.6418	1159	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862515.1	s__Asanoa iriomotensis	79.6266	1315	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868155.1	s__Micromonospora sp008868155	79.6064	1075	3382	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	79.5864	1186	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000982955.1	s__Micromonospora sp000982955	79.5608	1204	3382	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	79.4918	1194	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	79.425	1169	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008119785.1	s__Micromonospora sp008119785	79.3748	1274	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	79.2117	1149	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107455.1	s__Asanoa ishikariensis	79.1631	1338	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014648355.1	s__Actinoplanes azureus	78.5732	1129	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	78.2899	1313	3382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,249] [INFO] GTDB search result was written to GCF_011764565.1_ASM1176456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:21,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:21,260] [INFO] DFAST_QC result json was written to GCF_011764565.1_ASM1176456v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:21,261] [INFO] DFAST_QC completed!
[2024-01-24 13:50:21,266] [INFO] Total running time: 0h4m36s