[2024-01-24 13:32:34,873] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference
[2024-01-24 13:32:36,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,301] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d2c4d14-f0ce-443f-87ac-2bf9bb4d0408/GCF_000585375.1_ASM58537v1_genomic.fna.gz | prodigal -d GCF_000585375.1_ASM58537v1_genomic.fna/cds.fna -a GCF_000585375.1_ASM58537v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:02,159] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:02,159] [INFO] Task started: HMMsearch
[2024-01-24 13:33:02,160] [INFO] Running command: hmmsearch --tblout GCF_000585375.1_ASM58537v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference/reference_markers.hmm GCF_000585375.1_ASM58537v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:02,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:02,743] [INFO] Found 6/6 markers.
[2024-01-24 13:33:02,819] [INFO] Query marker FASTA was written to GCF_000585375.1_ASM58537v1_genomic.fna/markers.fasta
[2024-01-24 13:33:02,820] [INFO] Task started: Blastn
[2024-01-24 13:33:02,820] [INFO] Running command: blastn -query GCF_000585375.1_ASM58537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference/reference_markers.fasta -out GCF_000585375.1_ASM58537v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:04,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:04,170] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:04,171] [INFO] Target genome list was writen to GCF_000585375.1_ASM58537v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:04,187] [INFO] Task started: fastANI
[2024-01-24 13:33:04,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d2c4d14-f0ce-443f-87ac-2bf9bb4d0408/GCF_000585375.1_ASM58537v1_genomic.fna.gz --refList GCF_000585375.1_ASM58537v1_genomic.fna/target_genomes.txt --output GCF_000585375.1_ASM58537v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:33,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:33,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:33,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:33,124] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:33,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:33,125] [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
Cryptosporangium arvum	strain=DSM 44712	GCA_000585375.1	80871	80871	type	True	100.0	3065	3065	95	conclusive
Cryptosporangium aurantiacum	strain=DSM 46144	GCA_900143005.1	134849	134849	type	True	83.39	1944	3065	95	below_threshold
Cryptosporangium phraense	strain=A-T 5661	GCA_006912135.1	2593070	2593070	type	True	83.3018	1828	3065	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	76.8227	709	3065	95	below_threshold
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	76.6437	1175	3065	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	76.5851	751	3065	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	76.5479	616	3065	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	76.5376	923	3065	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	76.5044	694	3065	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	76.4923	1042	3065	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	76.2951	667	3065	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	76.1568	765	3065	95	below_threshold
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	76.0979	835	3065	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	76.0421	757	3065	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	75.6818	376	3065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,127] [INFO] DFAST Taxonomy check result was written to GCF_000585375.1_ASM58537v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:33,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:33,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:33,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference/checkm_data
[2024-01-24 13:33:33,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:33,211] [INFO] Task started: CheckM
[2024-01-24 13:33:33,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000585375.1_ASM58537v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000585375.1_ASM58537v1_genomic.fna/checkm_input GCF_000585375.1_ASM58537v1_genomic.fna/checkm_result
[2024-01-24 13:34:58,154] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:58,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:58,185] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:58,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:58,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000585375.1_ASM58537v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:58,186] [INFO] Task started: Blastn
[2024-01-24 13:34:58,186] [INFO] Running command: blastn -query GCF_000585375.1_ASM58537v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5953bb05-a6c7-49a7-adc5-2d2985b62c26/dqc_reference/reference_markers_gtdb.fasta -out GCF_000585375.1_ASM58537v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:00,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:00,085] [INFO] Selected 15 target genomes.
[2024-01-24 13:35:00,085] [INFO] Target genome list was writen to GCF_000585375.1_ASM58537v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:00,174] [INFO] Task started: fastANI
[2024-01-24 13:35:00,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d2c4d14-f0ce-443f-87ac-2bf9bb4d0408/GCF_000585375.1_ASM58537v1_genomic.fna.gz --refList GCF_000585375.1_ASM58537v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000585375.1_ASM58537v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:29,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:29,198] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:29,199] [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_000585375.1	s__Cryptosporangium arvum	100.0	3065	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900143005.1	s__Cryptosporangium aurantiacum	83.4023	1941	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006912135.1	s__Cryptosporangium phraense	83.284	1830	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Cryptosporangiaceae;g__Cryptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172955.1	s__Micromonospora sp003172955	76.7973	719	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	76.6842	638	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	76.6523	940	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863635.1	s__Virgisporangium aurantiacum	76.6281	1180	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862555.1	s__Asanoa siamensis	76.5453	921	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	76.4985	1041	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993745.1	s__Fodinicola acaciae	76.4503	699	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__HKI-0501;g__Fodinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203325.1	s__Saccharopolyspora_C gloriosae	76.348	697	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013870525.1	s__Amycolatopsis pittospori	76.2933	671	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200435.1	s__Sphaerisporangium krabiense	76.1438	780	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015711605.1	s__Planomonospora_A sp015711605	76.1428	769	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372745.1	s__Embleya scabrispora	76.1285	819	3065	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Embleya	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:29,202] [INFO] GTDB search result was written to GCF_000585375.1_ASM58537v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:29,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:29,207] [INFO] DFAST_QC result json was written to GCF_000585375.1_ASM58537v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:29,207] [INFO] DFAST_QC completed!
[2024-01-24 13:35:29,207] [INFO] Total running time: 0h2m54s