[2024-01-25 17:39:20,778] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:20,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:20,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference
[2024-01-25 17:39:21,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:21,988] [INFO] Task started: Prodigal
[2024-01-25 17:39:21,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg12706c26-aae3-48c7-9b27-0bdf3dac2c69/GCF_900447535.1_50279_C01_genomic.fna.gz | prodigal -d GCF_900447535.1_50279_C01_genomic.fna/cds.fna -a GCF_900447535.1_50279_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:30,233] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:30,233] [INFO] Task started: HMMsearch
[2024-01-25 17:39:30,233] [INFO] Running command: hmmsearch --tblout GCF_900447535.1_50279_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference/reference_markers.hmm GCF_900447535.1_50279_C01_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:30,453] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:30,455] [INFO] Found 6/6 markers.
[2024-01-25 17:39:30,479] [INFO] Query marker FASTA was written to GCF_900447535.1_50279_C01_genomic.fna/markers.fasta
[2024-01-25 17:39:30,480] [INFO] Task started: Blastn
[2024-01-25 17:39:30,480] [INFO] Running command: blastn -query GCF_900447535.1_50279_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference/reference_markers.fasta -out GCF_900447535.1_50279_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:31,641] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:31,643] [INFO] Selected 17 target genomes.
[2024-01-25 17:39:31,644] [INFO] Target genome list was writen to GCF_900447535.1_50279_C01_genomic.fna/target_genomes.txt
[2024-01-25 17:39:31,666] [INFO] Task started: fastANI
[2024-01-25 17:39:31,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg12706c26-aae3-48c7-9b27-0bdf3dac2c69/GCF_900447535.1_50279_C01_genomic.fna.gz --refList GCF_900447535.1_50279_C01_genomic.fna/target_genomes.txt --output GCF_900447535.1_50279_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:43,958] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:43,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:43,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:43,970] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:39:43,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:43,971] [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
Dermacoccus nishinomiyaensis	strain=NCTC11039	GCA_900447535.1	1274	1274	type	True	100.0	1026	1032	95	conclusive
Dermacoccus nishinomiyaensis	strain=FDAARGOS_1119	GCA_016766835.1	1274	1274	type	True	99.9996	1013	1032	95	conclusive
Dermacoccus abyssi	strain=MT1.1	GCA_003515945.1	322596	322596	type	True	83.9457	695	1032	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.3272	418	1032	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	79.1219	390	1032	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	79.0122	402	1032	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.6515	304	1032	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.5977	369	1032	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	78.5805	341	1032	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	78.5568	372	1032	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.3413	326	1032	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.2584	320	1032	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.2368	268	1032	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.6439	245	1032	95	below_threshold
Cellulomonas oligotrophica	strain=DSM 24482	GCA_013409875.1	931536	931536	type	True	77.3127	279	1032	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	77.1879	239	1032	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.1028	304	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:43,972] [INFO] DFAST Taxonomy check result was written to GCF_900447535.1_50279_C01_genomic.fna/tc_result.tsv
[2024-01-25 17:39:43,972] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:43,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:43,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference/checkm_data
[2024-01-25 17:39:43,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:44,006] [INFO] Task started: CheckM
[2024-01-25 17:39:44,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447535.1_50279_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447535.1_50279_C01_genomic.fna/checkm_input GCF_900447535.1_50279_C01_genomic.fna/checkm_result
[2024-01-25 17:40:26,415] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:26,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:26,437] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:26,437] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:26,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447535.1_50279_C01_genomic.fna/markers.fasta)
[2024-01-25 17:40:26,438] [INFO] Task started: Blastn
[2024-01-25 17:40:26,439] [INFO] Running command: blastn -query GCF_900447535.1_50279_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7b07ed6-2b15-4e15-93f1-14b71f7948c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447535.1_50279_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:28,323] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:28,326] [INFO] Selected 22 target genomes.
[2024-01-25 17:40:28,326] [INFO] Target genome list was writen to GCF_900447535.1_50279_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:28,346] [INFO] Task started: fastANI
[2024-01-25 17:40:28,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg12706c26-aae3-48c7-9b27-0bdf3dac2c69/GCF_900447535.1_50279_C01_genomic.fna.gz --refList GCF_900447535.1_50279_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447535.1_50279_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:45,438] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:45,451] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:45,452] [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_900447535.1	s__Dermacoccus nishinomiyaensis	100.0	1027	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Dermacoccus	95.0	98.76	98.05	0.93	0.90	18	conclusive
GCF_003515945.1	s__Dermacoccus abyssi	83.9591	694	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Dermacoccus	95.0	97.58	97.20	0.89	0.88	6	-
GCF_001247745.1	s__Luteipulveratus halotolerans	79.3275	418	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	79.081	389	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.7869	335	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715875.1	s__Terrabacter sp006715875	78.7591	365	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383675.1	s__Terrabacter sp000383675	78.646	382	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.6432	365	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_006715095.1	s__Yimella lutea	78.6345	318	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.40	98.40	0.90	0.90	2	-
GCA_000620545.1	s__Terrabacter sp000620545	78.5955	332	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	78.5726	341	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111375.1	s__Pedococcus cremeus	78.5622	355	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_007992835.1	s__Knoellia locipacati	78.5453	343	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991735.1	s__Terrabacter aerolatus	78.5293	386	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	78.506	387	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	78.4987	389	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCF_001428025.1	s__Pedococcus sp001428025	78.4089	324	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297495.1	s__Janibacter hoylei	78.2784	334	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001428065.1	s__Phycicoccus sp001428065	78.2346	308	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	78.1665	310	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	78.1445	344	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	78.1123	398	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:45,453] [INFO] GTDB search result was written to GCF_900447535.1_50279_C01_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:45,453] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:45,457] [INFO] DFAST_QC result json was written to GCF_900447535.1_50279_C01_genomic.fna/dqc_result.json
[2024-01-25 17:40:45,457] [INFO] DFAST_QC completed!
[2024-01-25 17:40:45,458] [INFO] Total running time: 0h1m25s