[2023-06-30 06:45:23,795] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:45:23,798] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:45:23,798] [INFO] DQC Reference Directory: /var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference
[2023-06-30 06:45:25,031] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:45:25,032] [INFO] Task started: Prodigal
[2023-06-30 06:45:25,032] [INFO] Running command: gunzip -c /var/lib/cwl/stg2450bf21-c7b3-471d-95e1-4a8d2feac930/GCA_025929295.1_ASM2592929v1_genomic.fna.gz | prodigal -d GCA_025929295.1_ASM2592929v1_genomic.fna/cds.fna -a GCA_025929295.1_ASM2592929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:45:33,803] [INFO] Task succeeded: Prodigal
[2023-06-30 06:45:33,804] [INFO] Task started: HMMsearch
[2023-06-30 06:45:33,804] [INFO] Running command: hmmsearch --tblout GCA_025929295.1_ASM2592929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference/reference_markers.hmm GCA_025929295.1_ASM2592929v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:45:34,014] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:45:34,016] [INFO] Found 6/6 markers.
[2023-06-30 06:45:34,047] [INFO] Query marker FASTA was written to GCA_025929295.1_ASM2592929v1_genomic.fna/markers.fasta
[2023-06-30 06:45:34,048] [INFO] Task started: Blastn
[2023-06-30 06:45:34,048] [INFO] Running command: blastn -query GCA_025929295.1_ASM2592929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference/reference_markers.fasta -out GCA_025929295.1_ASM2592929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:45:35,228] [INFO] Task succeeded: Blastn
[2023-06-30 06:45:35,232] [INFO] Selected 26 target genomes.
[2023-06-30 06:45:35,232] [INFO] Target genome list was writen to GCA_025929295.1_ASM2592929v1_genomic.fna/target_genomes.txt
[2023-06-30 06:45:35,238] [INFO] Task started: fastANI
[2023-06-30 06:45:35,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg2450bf21-c7b3-471d-95e1-4a8d2feac930/GCA_025929295.1_ASM2592929v1_genomic.fna.gz --refList GCA_025929295.1_ASM2592929v1_genomic.fna/target_genomes.txt --output GCA_025929295.1_ASM2592929v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:45:56,007] [INFO] Task succeeded: fastANI
[2023-06-30 06:45:56,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:45:56,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:45:56,027] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:45:56,027] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 06:45:56,028] [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 panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	82.1033	664	1048	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	80.1287	547	1048	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.2475	472	1048	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	79.2151	424	1048	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.2057	431	1048	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.1013	428	1048	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	79.0983	454	1048	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	79.0658	483	1048	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	78.9419	462	1048	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	78.9393	455	1048	95	below_threshold
Nocardioides massiliensis	strain=GD13	GCA_900067705.2	1325935	1325935	type	True	78.9334	289	1048	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	78.8979	425	1048	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	78.844	455	1048	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	78.7601	411	1048	95	below_threshold
Nocardioides cynanchi	strain=SB3-45	GCA_008761635.1	2558918	2558918	type	True	78.7472	428	1048	95	below_threshold
Nocardioides agariphilus	strain=KCTC 19276	GCA_015352445.1	433664	433664	type	True	78.7446	397	1048	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	78.6964	440	1048	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	78.6931	425	1048	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	78.6651	470	1048	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	78.6601	421	1048	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	78.55	358	1048	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	78.4773	388	1048	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	78.4755	412	1048	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	78.4181	405	1048	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	78.2652	291	1048	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	78.2033	395	1048	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 06:45:56,031] [INFO] DFAST Taxonomy check result was written to GCA_025929295.1_ASM2592929v1_genomic.fna/tc_result.tsv
[2023-06-30 06:45:56,031] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:45:56,032] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:45:56,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference/checkm_data
[2023-06-30 06:45:56,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:45:56,070] [INFO] Task started: CheckM
[2023-06-30 06:45:56,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025929295.1_ASM2592929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025929295.1_ASM2592929v1_genomic.fna/checkm_input GCA_025929295.1_ASM2592929v1_genomic.fna/checkm_result
[2023-06-30 06:46:38,726] [INFO] Task succeeded: CheckM
[2023-06-30 06:46:38,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:46:38,741] [INFO] ===== Completeness check finished =====
[2023-06-30 06:46:38,741] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:46:38,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025929295.1_ASM2592929v1_genomic.fna/markers.fasta)
[2023-06-30 06:46:38,742] [INFO] Task started: Blastn
[2023-06-30 06:46:38,742] [INFO] Running command: blastn -query GCA_025929295.1_ASM2592929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba1a27d2-ac94-4c01-9b92-372bea24bb44/dqc_reference/reference_markers_gtdb.fasta -out GCA_025929295.1_ASM2592929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:46:40,544] [INFO] Task succeeded: Blastn
[2023-06-30 06:46:40,547] [INFO] Selected 21 target genomes.
[2023-06-30 06:46:40,548] [INFO] Target genome list was writen to GCA_025929295.1_ASM2592929v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:46:40,559] [INFO] Task started: fastANI
[2023-06-30 06:46:40,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg2450bf21-c7b3-471d-95e1-4a8d2feac930/GCA_025929295.1_ASM2592929v1_genomic.fna.gz --refList GCA_025929295.1_ASM2592929v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025929295.1_ASM2592929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:46:57,344] [INFO] Task succeeded: fastANI
[2023-06-30 06:46:57,361] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 06:46:57,361] [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_019039255.1	s__JABFXA01 sp019039255	82.0949	664	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	81.0843	539	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_014395785.1	s__Nocardioides_B mesophilus	80.6765	540	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	80.1191	548	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384855.1	s__UBA4001 sp002384855	79.5167	430	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	79.2326	474	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	79.2066	431	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127485.1	s__Nocardioides sp014127485	79.1942	426	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	79.0728	484	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424755.1	s__Marmoricola sp001424755	79.0708	447	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752505.1	s__Marmoricola aurantiacus	79.0647	431	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426045.1	s__Marmoricola sp000426045	79.0216	450	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805855.1	s__UBA4001 sp902805855	79.0115	368	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	78.9413	462	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	78.9306	456	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725535.1	s__Marmoricola pocheonensis	78.7474	438	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352455.1	s__Nocardioides islandensis	78.6517	469	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865585.1	s__Nocardioides houyundeii	78.5566	356	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	-
GCF_014266025.1	s__Nocardioides deserti	78.552	443	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017354415.1	s__Nocardioides sp017354415	78.4189	332	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627335.1	s__Nocardioides sp001627335	78.3276	355	1048	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
--------------------------------------------------------------------------------
[2023-06-30 06:46:57,363] [INFO] GTDB search result was written to GCA_025929295.1_ASM2592929v1_genomic.fna/result_gtdb.tsv
[2023-06-30 06:46:57,363] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:46:57,368] [INFO] DFAST_QC result json was written to GCA_025929295.1_ASM2592929v1_genomic.fna/dqc_result.json
[2023-06-30 06:46:57,368] [INFO] DFAST_QC completed!
[2023-06-30 06:46:57,369] [INFO] Total running time: 0h1m34s