[2023-06-08 07:54:35,480] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:54:35,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:54:35,488] [INFO] DQC Reference Directory: /var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference
[2023-06-08 07:54:37,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:54:37,179] [INFO] Task started: Prodigal
[2023-06-08 07:54:37,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ff4cb7c-d102-4ae4-8453-9d8a754fb706/GCA_945877545.1_MoE-02may19-65_genomic.fna.gz | prodigal -d GCA_945877545.1_MoE-02may19-65_genomic.fna/cds.fna -a GCA_945877545.1_MoE-02may19-65_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:54:44,915] [INFO] Task succeeded: Prodigal
[2023-06-08 07:54:44,915] [INFO] Task started: HMMsearch
[2023-06-08 07:54:44,915] [INFO] Running command: hmmsearch --tblout GCA_945877545.1_MoE-02may19-65_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference/reference_markers.hmm GCA_945877545.1_MoE-02may19-65_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:54:45,099] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:54:45,100] [INFO] Found 6/6 markers.
[2023-06-08 07:54:45,130] [INFO] Query marker FASTA was written to GCA_945877545.1_MoE-02may19-65_genomic.fna/markers.fasta
[2023-06-08 07:54:45,130] [INFO] Task started: Blastn
[2023-06-08 07:54:45,131] [INFO] Running command: blastn -query GCA_945877545.1_MoE-02may19-65_genomic.fna/markers.fasta -db /var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference/reference_markers.fasta -out GCA_945877545.1_MoE-02may19-65_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:54:45,936] [INFO] Task succeeded: Blastn
[2023-06-08 07:54:45,940] [INFO] Selected 35 target genomes.
[2023-06-08 07:54:45,940] [INFO] Target genome list was writen to GCA_945877545.1_MoE-02may19-65_genomic.fna/target_genomes.txt
[2023-06-08 07:54:45,962] [INFO] Task started: fastANI
[2023-06-08 07:54:45,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff4cb7c-d102-4ae4-8453-9d8a754fb706/GCA_945877545.1_MoE-02may19-65_genomic.fna.gz --refList GCA_945877545.1_MoE-02may19-65_genomic.fna/target_genomes.txt --output GCA_945877545.1_MoE-02may19-65_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:55:10,993] [INFO] Task succeeded: fastANI
[2023-06-08 07:55:10,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:55:10,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:55:11,015] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:55:11,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:55:11,015] [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
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	76.7241	67	852	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	76.6761	52	852	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	76.5038	77	852	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	76.4144	57	852	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	76.4142	73	852	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	76.3792	57	852	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	76.3753	65	852	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	76.3725	76	852	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.3684	58	852	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	76.3517	63	852	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	76.303	69	852	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	76.303	69	852	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	76.296	70	852	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	76.2919	70	852	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	76.1801	69	852	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	76.1768	78	852	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.0813	58	852	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	76.0539	58	852	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.0446	66	852	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	75.9769	87	852	95	below_threshold
Sanguibacter suarezii	strain=NBRC 16159	GCA_001552735.1	60921	60921	type	True	75.9758	50	852	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	75.9156	51	852	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	75.9123	65	852	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.8861	74	852	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	75.8751	82	852	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	75.8346	54	852	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	75.8329	64	852	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	75.7411	59	852	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	75.6724	84	852	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	75.6272	59	852	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	75.5174	60	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:55:11,017] [INFO] DFAST Taxonomy check result was written to GCA_945877545.1_MoE-02may19-65_genomic.fna/tc_result.tsv
[2023-06-08 07:55:11,018] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:55:11,018] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:55:11,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference/checkm_data
[2023-06-08 07:55:11,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:55:11,047] [INFO] Task started: CheckM
[2023-06-08 07:55:11,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877545.1_MoE-02may19-65_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877545.1_MoE-02may19-65_genomic.fna/checkm_input GCA_945877545.1_MoE-02may19-65_genomic.fna/checkm_result
[2023-06-08 07:55:38,213] [INFO] Task succeeded: CheckM
[2023-06-08 07:55:38,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:55:38,230] [INFO] ===== Completeness check finished =====
[2023-06-08 07:55:38,231] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:55:38,231] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877545.1_MoE-02may19-65_genomic.fna/markers.fasta)
[2023-06-08 07:55:38,231] [INFO] Task started: Blastn
[2023-06-08 07:55:38,231] [INFO] Running command: blastn -query GCA_945877545.1_MoE-02may19-65_genomic.fna/markers.fasta -db /var/lib/cwl/stgf743db59-25f3-4a5a-937e-d78dd7f10bd6/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877545.1_MoE-02may19-65_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:55:39,369] [INFO] Task succeeded: Blastn
[2023-06-08 07:55:39,372] [INFO] Selected 22 target genomes.
[2023-06-08 07:55:39,372] [INFO] Target genome list was writen to GCA_945877545.1_MoE-02may19-65_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:55:39,380] [INFO] Task started: fastANI
[2023-06-08 07:55:39,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff4cb7c-d102-4ae4-8453-9d8a754fb706/GCA_945877545.1_MoE-02may19-65_genomic.fna.gz --refList GCA_945877545.1_MoE-02may19-65_genomic.fna/target_genomes_gtdb.txt --output GCA_945877545.1_MoE-02may19-65_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:55:52,399] [INFO] Task succeeded: fastANI
[2023-06-08 07:55:52,414] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 07:55:52,414] [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_009699015.1	s__WLND01 sp009699015	84.9857	594	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
GCA_009726075.1	s__WLND01 sp009726075	78.5946	237	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717115.1	s__UBA10649 sp016717115	77.7444	172	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903940375.1	s__UBA10649 sp903940375	77.6117	135	852	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_016125355.1	s__UBA10649 sp016125355	77.4112	149	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970025.1	s__REEB460 sp018970025	77.2954	150	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__REEB460	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908025.1	s__UBA10649 sp903908025	77.2889	151	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.87	97.91	0.84	0.77	3	-
GCA_017856385.1	s__UBA10649 sp017856385	77.2734	158	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125335.1	s__WLRQ01 sp016125335	76.9807	122	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__CAIYMF01;g__WLRQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849335.1	s__UBA10649 sp017849335	76.9114	99	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	76.6593	69	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870195.1	s__VGCC01 sp016870195	76.6455	84	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__VGCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903909555.1	s__Mxb001 sp903909555	76.4361	103	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	99.15	99.05	0.83	0.81	4	-
GCF_003047295.1	s__Nocardioides sediminis	76.3639	66	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097515.1	s__Streptomyces tirandamycinicus	76.3459	66	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	98.27	0.90	0.88	6	-
GCF_006346315.1	s__Nocardioides litoris	76.3226	82	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718255.1	s__Spirillospora albida	76.3025	60	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506375.1	s__Microbacterium sp902506375	76.0635	54	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	75.8485	74	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648675.1	s__Spirillospora livida	75.6948	73	852	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	98.54	97.09	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-08 07:55:52,416] [INFO] GTDB search result was written to GCA_945877545.1_MoE-02may19-65_genomic.fna/result_gtdb.tsv
[2023-06-08 07:55:52,416] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:55:52,421] [INFO] DFAST_QC result json was written to GCA_945877545.1_MoE-02may19-65_genomic.fna/dqc_result.json
[2023-06-08 07:55:52,421] [INFO] DFAST_QC completed!
[2023-06-08 07:55:52,421] [INFO] Total running time: 0h1m17s