[2024-01-24 15:27:41,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,302] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgabe9c386-04aa-4dc1-9a0d-1f63763b1d4c/GCF_014203715.1_ASM1420371v1_genomic.fna.gz | prodigal -d GCF_014203715.1_ASM1420371v1_genomic.fna/cds.fna -a GCF_014203715.1_ASM1420371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:28:08,374] [INFO] Task succeeded: Prodigal
[2024-01-24 15:28:08,375] [INFO] Task started: HMMsearch
[2024-01-24 15:28:08,375] [INFO] Running command: hmmsearch --tblout GCF_014203715.1_ASM1420371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference/reference_markers.hmm GCF_014203715.1_ASM1420371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:28:08,734] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:28:08,735] [INFO] Found 6/6 markers.
[2024-01-24 15:28:08,802] [INFO] Query marker FASTA was written to GCF_014203715.1_ASM1420371v1_genomic.fna/markers.fasta
[2024-01-24 15:28:08,802] [INFO] Task started: Blastn
[2024-01-24 15:28:08,802] [INFO] Running command: blastn -query GCF_014203715.1_ASM1420371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference/reference_markers.fasta -out GCF_014203715.1_ASM1420371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:10,112] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:10,116] [INFO] Selected 26 target genomes.
[2024-01-24 15:28:10,116] [INFO] Target genome list was writen to GCF_014203715.1_ASM1420371v1_genomic.fna/target_genomes.txt
[2024-01-24 15:28:10,128] [INFO] Task started: fastANI
[2024-01-24 15:28:10,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgabe9c386-04aa-4dc1-9a0d-1f63763b1d4c/GCF_014203715.1_ASM1420371v1_genomic.fna.gz --refList GCF_014203715.1_ASM1420371v1_genomic.fna/target_genomes.txt --output GCF_014203715.1_ASM1420371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:54,551] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:54,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:54,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:54,583] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:54,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:54,585] [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
Streptosporangium saharense	strain=CECT 8840	GCA_014203715.1	1706840	1706840	type	True	100.0	2816	2818	95	conclusive
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	84.2424	1623	2818	95	below_threshold
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	84.1619	1721	2818	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	84.1261	1590	2818	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	84.0829	1342	2818	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	83.4554	1454	2818	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	83.183	1457	2818	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	83.1037	1528	2818	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	82.7122	1352	2818	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=JCM 3094	GCA_014647955.1	97193	58119	type	True	82.6208	1387	2818	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	82.5756	1443	2818	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	82.5072	1439	2818	95	below_threshold
Planobispora siamensis	strain=NBRC 107568	GCA_016863175.1	936338	936338	type	True	82.5049	1464	2818	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	82.4886	1393	2818	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	82.4258	1378	2818	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	82.4091	1441	2818	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.0615	867	2818	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.9945	1332	2818	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.673	1272	2818	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.4328	997	2818	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	79.3265	1241	2818	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	76.7791	685	2818	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	76.4681	462	2818	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	76.3195	496	2818	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	76.2909	505	2818	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	76.2826	471	2818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:54,588] [INFO] DFAST Taxonomy check result was written to GCF_014203715.1_ASM1420371v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:54,589] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:54,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:54,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference/checkm_data
[2024-01-24 15:28:54,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:54,675] [INFO] Task started: CheckM
[2024-01-24 15:28:54,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203715.1_ASM1420371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203715.1_ASM1420371v1_genomic.fna/checkm_input GCF_014203715.1_ASM1420371v1_genomic.fna/checkm_result
[2024-01-24 15:30:12,704] [INFO] Task succeeded: CheckM
[2024-01-24 15:30:12,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 20.02%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 15:30:12,732] [INFO] ===== Completeness check finished =====
[2024-01-24 15:30:12,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:30:12,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203715.1_ASM1420371v1_genomic.fna/markers.fasta)
[2024-01-24 15:30:12,733] [INFO] Task started: Blastn
[2024-01-24 15:30:12,733] [INFO] Running command: blastn -query GCF_014203715.1_ASM1420371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0ec2e80-c887-4c38-869c-c6704efbede1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203715.1_ASM1420371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:30:14,803] [INFO] Task succeeded: Blastn
[2024-01-24 15:30:14,807] [INFO] Selected 18 target genomes.
[2024-01-24 15:30:14,808] [INFO] Target genome list was writen to GCF_014203715.1_ASM1420371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:30:14,820] [INFO] Task started: fastANI
[2024-01-24 15:30:14,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgabe9c386-04aa-4dc1-9a0d-1f63763b1d4c/GCF_014203715.1_ASM1420371v1_genomic.fna.gz --refList GCF_014203715.1_ASM1420371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203715.1_ASM1420371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:47,056] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:47,074] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:47,074] [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_014203715.1	s__Streptosporangium saharense	100.0	2816	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113865.1	s__Streptosporangium canum	84.2585	1619	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_002149035.1	s__Streptosporangium minutum	84.1417	1586	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_000024865.1	s__Streptosporangium roseum	84.1083	1731	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654615.1	s__Streptosporangium violaceochromogenes	84.0876	1342	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	83.4165	1461	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409935.1	s__Streptosporangium sandarakinum	83.1582	1461	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014648055.1	s__Streptosporangium pseudovulgare	83.1241	1525	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	96.6013	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	82.9179	1402	2818	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_016863195.1	s__Planobispora takensis	82.606	1438	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	82.5769	1407	2818	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_016863175.1	s__Planobispora siamensis	82.5136	1463	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.117	N/A	N/A	N/A	N/A	1	-
GCF_015711645.1	s__Planomonospora sp015711645	82.5068	1340	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	82.5036	1388	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_016863135.1	s__Planobispora longispora	82.4084	1439	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240215.1	s__Bog-532 sp019240215	76.7893	414	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141985.1	s__Nocardiopsis flavescens	76.7884	683	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319115.1	s__Geodermatophilus sp003319115	76.5159	497	2818	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:47,076] [INFO] GTDB search result was written to GCF_014203715.1_ASM1420371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:47,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:47,083] [INFO] DFAST_QC result json was written to GCF_014203715.1_ASM1420371v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:47,084] [INFO] DFAST_QC completed!
[2024-01-24 15:30:47,084] [INFO] Total running time: 0h3m6s