[2023-06-18 10:48:44,318] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:48:44,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:48:44,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference
[2023-06-18 10:48:46,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:48:46,143] [INFO] Task started: Prodigal
[2023-06-18 10:48:46,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ca5282a-8c25-4a20-ac83-7198b4faa22a/GCA_018402235.1_ASM1840223v1_genomic.fna.gz | prodigal -d GCA_018402235.1_ASM1840223v1_genomic.fna/cds.fna -a GCA_018402235.1_ASM1840223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:48:53,903] [INFO] Task succeeded: Prodigal
[2023-06-18 10:48:53,904] [INFO] Task started: HMMsearch
[2023-06-18 10:48:53,905] [INFO] Running command: hmmsearch --tblout GCA_018402235.1_ASM1840223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference/reference_markers.hmm GCA_018402235.1_ASM1840223v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:48:54,084] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:48:54,085] [INFO] Found 6/6 markers.
[2023-06-18 10:48:54,111] [INFO] Query marker FASTA was written to GCA_018402235.1_ASM1840223v1_genomic.fna/markers.fasta
[2023-06-18 10:48:54,111] [INFO] Task started: Blastn
[2023-06-18 10:48:54,111] [INFO] Running command: blastn -query GCA_018402235.1_ASM1840223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference/reference_markers.fasta -out GCA_018402235.1_ASM1840223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:48:54,854] [INFO] Task succeeded: Blastn
[2023-06-18 10:48:54,858] [INFO] Selected 35 target genomes.
[2023-06-18 10:48:54,859] [INFO] Target genome list was writen to GCA_018402235.1_ASM1840223v1_genomic.fna/target_genomes.txt
[2023-06-18 10:48:54,900] [INFO] Task started: fastANI
[2023-06-18 10:48:54,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca5282a-8c25-4a20-ac83-7198b4faa22a/GCA_018402235.1_ASM1840223v1_genomic.fna.gz --refList GCA_018402235.1_ASM1840223v1_genomic.fna/target_genomes.txt --output GCA_018402235.1_ASM1840223v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:49:25,968] [INFO] Task succeeded: fastANI
[2023-06-18 10:49:25,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:49:25,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:49:25,982] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:49:25,982] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 10:49:25,983] [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
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	77.024	51	732	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	76.8513	62	732	95	below_threshold
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	76.7096	56	732	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	76.6502	58	732	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	76.6462	54	732	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	76.3631	63	732	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	76.356	63	732	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	76.3326	54	732	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	76.2861	60	732	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	76.2311	63	732	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	76.2099	61	732	95	below_threshold
Streptomyces mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	76.1884	58	732	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	76.1688	58	732	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	76.1583	58	732	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	76.1507	50	732	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	76.1238	55	732	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	76.1122	63	732	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:49:25,985] [INFO] DFAST Taxonomy check result was written to GCA_018402235.1_ASM1840223v1_genomic.fna/tc_result.tsv
[2023-06-18 10:49:25,985] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:49:25,985] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:49:25,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference/checkm_data
[2023-06-18 10:49:25,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:49:26,010] [INFO] Task started: CheckM
[2023-06-18 10:49:26,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018402235.1_ASM1840223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018402235.1_ASM1840223v1_genomic.fna/checkm_input GCA_018402235.1_ASM1840223v1_genomic.fna/checkm_result
[2023-06-18 10:49:52,737] [INFO] Task succeeded: CheckM
[2023-06-18 10:49:52,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:49:52,757] [INFO] ===== Completeness check finished =====
[2023-06-18 10:49:52,758] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:49:52,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018402235.1_ASM1840223v1_genomic.fna/markers.fasta)
[2023-06-18 10:49:52,758] [INFO] Task started: Blastn
[2023-06-18 10:49:52,758] [INFO] Running command: blastn -query GCA_018402235.1_ASM1840223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg566e22f3-8f5e-41e6-8389-8658ea4a77f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_018402235.1_ASM1840223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:49:53,733] [INFO] Task succeeded: Blastn
[2023-06-18 10:49:53,738] [INFO] Selected 22 target genomes.
[2023-06-18 10:49:53,738] [INFO] Target genome list was writen to GCA_018402235.1_ASM1840223v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:49:53,826] [INFO] Task started: fastANI
[2023-06-18 10:49:53,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca5282a-8c25-4a20-ac83-7198b4faa22a/GCA_018402235.1_ASM1840223v1_genomic.fna.gz --refList GCA_018402235.1_ASM1840223v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018402235.1_ASM1840223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:50:05,549] [INFO] Task succeeded: fastANI
[2023-06-18 10:50:05,561] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:50:05,561] [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
GCA_018402235.1	s__S36-B12 sp018402235	100.0	732	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002728915.1	s__S36-B12 sp002728915	77.7871	139	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	99.13	98.99	0.85	0.80	4	-
GCA_002729215.1	s__S36-B12 sp002729215	77.6753	153	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.32	97.43	0.87	0.81	12	-
GCA_012103605.1	s__S36-B12 sp012103605	77.6602	147	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	95.57	95.57	0.76	0.76	2	-
GCA_010029945.1	s__S36-B12 sp010029945	77.604	137	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.25	98.18	0.79	0.75	5	-
GCA_002694095.1	s__S36-B12 sp002694095	77.3722	140	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	97.65	97.49	0.82	0.80	3	-
GCA_903934925.1	s__UBA10649 sp903934925	77.3379	97	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	99.42	99.35	0.85	0.83	4	-
GCA_016870515.1	s__Mxb001 sp016870515	77.0011	77	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903940375.1	s__UBA10649 sp903940375	76.8661	99	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.93	98.93	0.81	0.81	2	-
GCA_016870425.1	s__Mxb001 sp016870425	76.6529	89	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848435.1	s__Mxb001 sp903848435	76.5309	59	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	96.93	95.89	0.80	0.74	3	-
GCA_014190275.1	s__GCA-2737125 sp014190275	76.4517	50	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__GCA-2737125	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	76.3631	63	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270745.1	s__Jiangella muralis	76.2099	61	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	76.0193	57	732	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 10:50:05,563] [INFO] GTDB search result was written to GCA_018402235.1_ASM1840223v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:50:05,564] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:50:05,568] [INFO] DFAST_QC result json was written to GCA_018402235.1_ASM1840223v1_genomic.fna/dqc_result.json
[2023-06-18 10:50:05,568] [INFO] DFAST_QC completed!
[2023-06-18 10:50:05,568] [INFO] Total running time: 0h1m21s