[2023-06-29 15:23:30,011] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:23:30,013] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:23:30,013] [INFO] DQC Reference Directory: /var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference
[2023-06-29 15:23:31,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:23:31,348] [INFO] Task started: Prodigal
[2023-06-29 15:23:31,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg751bb352-f9d3-4fb9-ac96-6159be6fcea9/GCA_021778655.1_ASM2177865v1_genomic.fna.gz | prodigal -d GCA_021778655.1_ASM2177865v1_genomic.fna/cds.fna -a GCA_021778655.1_ASM2177865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:23:35,659] [INFO] Task succeeded: Prodigal
[2023-06-29 15:23:35,659] [INFO] Task started: HMMsearch
[2023-06-29 15:23:35,660] [INFO] Running command: hmmsearch --tblout GCA_021778655.1_ASM2177865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference/reference_markers.hmm GCA_021778655.1_ASM2177865v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:23:35,879] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:23:35,880] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg751bb352-f9d3-4fb9-ac96-6159be6fcea9/GCA_021778655.1_ASM2177865v1_genomic.fna.gz]
[2023-06-29 15:23:35,904] [INFO] Query marker FASTA was written to GCA_021778655.1_ASM2177865v1_genomic.fna/markers.fasta
[2023-06-29 15:23:35,905] [INFO] Task started: Blastn
[2023-06-29 15:23:35,905] [INFO] Running command: blastn -query GCA_021778655.1_ASM2177865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference/reference_markers.fasta -out GCA_021778655.1_ASM2177865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:23:36,702] [INFO] Task succeeded: Blastn
[2023-06-29 15:23:36,708] [INFO] Selected 25 target genomes.
[2023-06-29 15:23:36,709] [INFO] Target genome list was writen to GCA_021778655.1_ASM2177865v1_genomic.fna/target_genomes.txt
[2023-06-29 15:23:36,713] [INFO] Task started: fastANI
[2023-06-29 15:23:36,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg751bb352-f9d3-4fb9-ac96-6159be6fcea9/GCA_021778655.1_ASM2177865v1_genomic.fna.gz --refList GCA_021778655.1_ASM2177865v1_genomic.fna/target_genomes.txt --output GCA_021778655.1_ASM2177865v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:23:53,098] [INFO] Task succeeded: fastANI
[2023-06-29 15:23:53,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:23:53,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:23:53,122] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:23:53,122] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:23:53,123] [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
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	77.8784	118	378	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	77.8734	111	378	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	77.7914	138	378	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	77.5547	114	378	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	77.5386	109	378	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.2823	116	378	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	76.8299	85	378	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	76.7485	50	378	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.7218	93	378	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	76.7217	72	378	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	76.6337	79	378	95	below_threshold
Tessaracoccus flavescens	strain=SST-39T	GCA_001998865.1	399497	399497	type	True	76.488	55	378	95	below_threshold
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	76.4323	63	378	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	76.3739	82	378	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	76.3716	104	378	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	76.3319	70	378	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	76.2406	93	378	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	76.2399	62	378	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	76.208	83	378	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	76.1685	85	378	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	76.1023	69	378	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	76.101	103	378	95	below_threshold
Carbonactinospora thermoautotrophica	strain=UBT1	GCA_001543895.1	1469144	1469144	type	True	76.0316	61	378	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.6664	93	378	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:23:53,125] [INFO] DFAST Taxonomy check result was written to GCA_021778655.1_ASM2177865v1_genomic.fna/tc_result.tsv
[2023-06-29 15:23:53,126] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:23:53,126] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:23:53,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference/checkm_data
[2023-06-29 15:23:53,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:23:53,152] [INFO] Task started: CheckM
[2023-06-29 15:23:53,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021778655.1_ASM2177865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021778655.1_ASM2177865v1_genomic.fna/checkm_input GCA_021778655.1_ASM2177865v1_genomic.fna/checkm_result
[2023-06-29 15:24:13,037] [INFO] Task succeeded: CheckM
[2023-06-29 15:24:13,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.47%
Contamintation: 3.47%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:24:13,063] [INFO] ===== Completeness check finished =====
[2023-06-29 15:24:13,063] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:24:13,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021778655.1_ASM2177865v1_genomic.fna/markers.fasta)
[2023-06-29 15:24:13,064] [INFO] Task started: Blastn
[2023-06-29 15:24:13,064] [INFO] Running command: blastn -query GCA_021778655.1_ASM2177865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge44e67a8-dfcf-4bec-b2d9-136799374243/dqc_reference/reference_markers_gtdb.fasta -out GCA_021778655.1_ASM2177865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:24:14,284] [INFO] Task succeeded: Blastn
[2023-06-29 15:24:14,290] [INFO] Selected 23 target genomes.
[2023-06-29 15:24:14,290] [INFO] Target genome list was writen to GCA_021778655.1_ASM2177865v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:24:14,307] [INFO] Task started: fastANI
[2023-06-29 15:24:14,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg751bb352-f9d3-4fb9-ac96-6159be6fcea9/GCA_021778655.1_ASM2177865v1_genomic.fna.gz --refList GCA_021778655.1_ASM2177865v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021778655.1_ASM2177865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:24:27,844] [INFO] Task succeeded: fastANI
[2023-06-29 15:24:27,873] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:24:27,874] [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_003153855.1	s__Fen-668 sp003153855	83.411	159	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	99.46	99.46	0.91	0.91	2	-
GCA_003158895.1	s__Fen-668 sp003158895	83.0399	168	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882655.1	s__Fen-668 sp017882655	81.693	132	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213595.1	s__Fen-668 sp016213595	80.4435	134	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001046855.1	s__Tetrasphaera japonica	78.0362	146	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Tetrasphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326735.1	s__Phycicoccus endophyticus	77.893	124	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_018139485.1	s__Phycicoccus sp018139485	77.8556	133	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	77.7757	143	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438965.1	s__Pedococcus bigeumensis	77.6243	102	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	77.5547	114	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	77.3816	132	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	77.3001	131	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429605.1	s__Pedococcus sp001429605	77.2616	108	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.23	98.23	0.91	0.91	2	-
GCA_013693855.1	s__Micropruina sp013693855	76.8566	58	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011393335.1	s__Brevilactibacter coleopterorum	76.7217	72	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193425.1	s__Friedmanniella antarctica	76.6109	80	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	76.5351	64	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110855.1	s__Friedmanniella flava	76.3744	105	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564375.1	s__Nocardioides euryhalodurans	76.3739	82	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105065.1	s__Friedmanniella luteola	76.3355	91	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306015.1	s__Propionicimonas sp017306015	76.2853	73	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907175.1	s__Friedmanniella spumicola	76.1954	86	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543895.1	s__Carbonactinospora thermoautotrophica	76.008	62	378	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Carbonactinosporaceae;g__Carbonactinospora	95.0	99.44	99.44	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-29 15:24:27,876] [INFO] GTDB search result was written to GCA_021778655.1_ASM2177865v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:24:27,876] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:24:27,881] [INFO] DFAST_QC result json was written to GCA_021778655.1_ASM2177865v1_genomic.fna/dqc_result.json
[2023-06-29 15:24:27,882] [INFO] DFAST_QC completed!
[2023-06-29 15:24:27,882] [INFO] Total running time: 0h0m58s