[2024-01-24 10:57:07,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference
[2024-01-24 10:57:08,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,764] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg24a3451d-8826-4c12-bd18-f137b4020fe2/GCF_016862835.1_ASM1686283v1_genomic.fna.gz | prodigal -d GCF_016862835.1_ASM1686283v1_genomic.fna/cds.fna -a GCF_016862835.1_ASM1686283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:34,296] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:34,297] [INFO] Task started: HMMsearch
[2024-01-24 10:57:34,297] [INFO] Running command: hmmsearch --tblout GCF_016862835.1_ASM1686283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference/reference_markers.hmm GCF_016862835.1_ASM1686283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:34,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:34,669] [INFO] Found 6/6 markers.
[2024-01-24 10:57:34,738] [INFO] Query marker FASTA was written to GCF_016862835.1_ASM1686283v1_genomic.fna/markers.fasta
[2024-01-24 10:57:34,739] [INFO] Task started: Blastn
[2024-01-24 10:57:34,739] [INFO] Running command: blastn -query GCF_016862835.1_ASM1686283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference/reference_markers.fasta -out GCF_016862835.1_ASM1686283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:36,003] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:36,007] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:36,008] [INFO] Target genome list was writen to GCF_016862835.1_ASM1686283v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:36,016] [INFO] Task started: fastANI
[2024-01-24 10:57:36,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg24a3451d-8826-4c12-bd18-f137b4020fe2/GCF_016862835.1_ASM1686283v1_genomic.fna.gz --refList GCF_016862835.1_ASM1686283v1_genomic.fna/target_genomes.txt --output GCF_016862835.1_ASM1686283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:12,343] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:12,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:12,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:12,365] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:12,365] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:12,365] [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
Longispora fulva	strain=NBRC 105670	GCA_016862835.1	619741	619741	type	True	100.0	2834	2836	95	conclusive
Longispora fulva	strain=DSM 45356	GCA_015751905.1	619741	619741	type	True	99.9991	2836	2836	95	conclusive
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	80.9006	1189	2836	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	77.7461	912	2836	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	77.6743	791	2836	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	77.6296	960	2836	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	77.611	865	2836	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	77.5982	978	2836	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	77.2377	948	2836	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	77.08	868	2836	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	77.0735	1097	2836	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	77.0177	851	2836	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	77.0176	898	2836	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	77.0085	876	2836	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	76.7314	558	2836	95	below_threshold
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	76.715	957	2836	95	below_threshold
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	76.5973	1020	2836	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	76.3732	799	2836	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	76.1895	566	2836	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.1725	555	2836	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	75.7102	213	2836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,367] [INFO] DFAST Taxonomy check result was written to GCF_016862835.1_ASM1686283v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:12,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:12,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:12,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference/checkm_data
[2024-01-24 10:58:12,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:12,445] [INFO] Task started: CheckM
[2024-01-24 10:58:12,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862835.1_ASM1686283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862835.1_ASM1686283v1_genomic.fna/checkm_input GCF_016862835.1_ASM1686283v1_genomic.fna/checkm_result
[2024-01-24 10:59:31,261] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:31,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:31,289] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:31,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:31,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862835.1_ASM1686283v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:31,289] [INFO] Task started: Blastn
[2024-01-24 10:59:31,290] [INFO] Running command: blastn -query GCF_016862835.1_ASM1686283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e48907a-f372-4069-86ca-c0a2c06735e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862835.1_ASM1686283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:33,118] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:33,123] [INFO] Selected 26 target genomes.
[2024-01-24 10:59:33,123] [INFO] Target genome list was writen to GCF_016862835.1_ASM1686283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:33,140] [INFO] Task started: fastANI
[2024-01-24 10:59:33,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg24a3451d-8826-4c12-bd18-f137b4020fe2/GCF_016862835.1_ASM1686283v1_genomic.fna.gz --refList GCF_016862835.1_ASM1686283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862835.1_ASM1686283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:14,929] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:14,953] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:14,953] [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_015751905.1	s__Longispora fulva	99.9991	2836	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Longispora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000379825.1	s__Longispora albida	80.9231	1187	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Longispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667505.1	s__Micromonospora sp003667505	77.8731	752	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_009720365.1	s__Catellatospora paridis	77.7227	919	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	77.7173	713	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018070045.1	s__Micromonospora sp018070045	77.6763	807	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862575.1	s__Catellatospora bangladeshensis	77.6717	974	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	95.24	95.24	0.85	0.85	2	-
GCA_003610235.1	s__Catellatospora citrea	77.6101	984	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	97.34	95.99	0.88	0.83	4	-
GCF_900143515.1	s__Micromonospora cremea	77.6009	866	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011947195.1	s__Planosporangium thailandense	77.5808	729	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	77.5309	860	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	77.2615	942	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	77.2479	882	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188005.1	s__Actinoplanes regularis	77.1519	837	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862795.1	s__Dactylosporangium siamense	77.101	1085	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	77.0238	893	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862175.1	s__Actinoplanes durhamensis	77.0145	911	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001815.1	s__Actinoplanes italicus	76.9998	878	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016862315.1	s__Actinoplanes palleronii	76.9752	961	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_003426775.1	s__Allorhizocola rhizosphaerae	76.72	561	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allorhizocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863655.1	s__Virgisporangium ochraceum	76.7134	957	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863635.1	s__Virgisporangium aurantiacum	76.6078	1016	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.4769	574	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716785.1	s__Thermopolyspora flexuosa	76.1833	569	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001046855.1	s__Tetrasphaera japonica	75.8824	375	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Tetrasphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:14,955] [INFO] GTDB search result was written to GCF_016862835.1_ASM1686283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:14,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:14,960] [INFO] DFAST_QC result json was written to GCF_016862835.1_ASM1686283v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:14,960] [INFO] DFAST_QC completed!
[2024-01-24 11:00:14,960] [INFO] Total running time: 0h3m7s