[2024-01-25 19:47:20,565] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference
[2024-01-25 19:47:21,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,717] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg31fa5233-8208-4038-abfa-b32afd67a4fb/GCF_031296655.1_ASM3129665v1_genomic.fna.gz | prodigal -d GCF_031296655.1_ASM3129665v1_genomic.fna/cds.fna -a GCF_031296655.1_ASM3129665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:29,768] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:29,768] [INFO] Task started: HMMsearch
[2024-01-25 19:47:29,768] [INFO] Running command: hmmsearch --tblout GCF_031296655.1_ASM3129665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference/reference_markers.hmm GCF_031296655.1_ASM3129665v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:29,996] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:29,997] [INFO] Found 6/6 markers.
[2024-01-25 19:47:30,029] [INFO] Query marker FASTA was written to GCF_031296655.1_ASM3129665v1_genomic.fna/markers.fasta
[2024-01-25 19:47:30,029] [INFO] Task started: Blastn
[2024-01-25 19:47:30,030] [INFO] Running command: blastn -query GCF_031296655.1_ASM3129665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference/reference_markers.fasta -out GCF_031296655.1_ASM3129665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:31,027] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:31,030] [INFO] Selected 13 target genomes.
[2024-01-25 19:47:31,031] [INFO] Target genome list was writen to GCF_031296655.1_ASM3129665v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:31,040] [INFO] Task started: fastANI
[2024-01-25 19:47:31,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg31fa5233-8208-4038-abfa-b32afd67a4fb/GCF_031296655.1_ASM3129665v1_genomic.fna.gz --refList GCF_031296655.1_ASM3129665v1_genomic.fna/target_genomes.txt --output GCF_031296655.1_ASM3129665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:39,763] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:39,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:39,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:39,773] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:47:39,773] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:39,774] [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
Actinomyces naeslundii	strain=NCTC 10301	GCA_001956585.1	1655	1655	type	True	99.993	1003	1024	95	conclusive
Actinomyces naeslundii	strain=Howell 279	GCA_000285995.1	1655	1655	type	True	99.8157	888	1024	95	conclusive
Actinomyces johnsonii	strain=CCUG 34287	GCA_006546835.1	544581	544581	type	True	89.75	873	1024	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287T	GCA_008693165.1	544581	544581	type	True	89.7025	873	1024	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	89.6507	860	1024	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	89.5939	867	1024	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	89.5845	879	1024	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	89.5775	867	1024	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	81.2835	427	1024	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	81.2579	488	1024	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.9192	263	1024	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	77.2858	162	1024	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.8215	197	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:39,776] [INFO] DFAST Taxonomy check result was written to GCF_031296655.1_ASM3129665v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:39,776] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:39,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:39,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference/checkm_data
[2024-01-25 19:47:39,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:39,809] [INFO] Task started: CheckM
[2024-01-25 19:47:39,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031296655.1_ASM3129665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031296655.1_ASM3129665v1_genomic.fna/checkm_input GCF_031296655.1_ASM3129665v1_genomic.fna/checkm_result
[2024-01-25 19:48:08,624] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:08,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:08,642] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:08,642] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:08,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031296655.1_ASM3129665v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:08,643] [INFO] Task started: Blastn
[2024-01-25 19:48:08,643] [INFO] Running command: blastn -query GCF_031296655.1_ASM3129665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cfc356a-37a3-44f0-a18c-4adb1e052dc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_031296655.1_ASM3129665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:10,196] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:10,199] [INFO] Selected 12 target genomes.
[2024-01-25 19:48:10,199] [INFO] Target genome list was writen to GCF_031296655.1_ASM3129665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:10,209] [INFO] Task started: fastANI
[2024-01-25 19:48:10,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg31fa5233-8208-4038-abfa-b32afd67a4fb/GCF_031296655.1_ASM3129665v1_genomic.fna.gz --refList GCF_031296655.1_ASM3129665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031296655.1_ASM3129665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:19,266] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:19,278] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:19,278] [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_001956585.1	s__Actinomyces naeslundii	99.993	1003	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.74	96.59	0.92	0.89	23	conclusive
GCF_001937665.1	s__Actinomyces oris_D	90.523	874	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195595.1	s__Actinomyces sp000195595	90.1695	868	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323545.1	s__Actinomyces sp900323545	90.0868	874	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.47	98.47	0.94	0.94	2	-
GCF_006546835.1	s__Actinomyces johnsonii	89.7535	872	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.09	97.12	0.94	0.92	6	-
GCF_005696555.1	s__Actinomyces oris_E	89.7465	855	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.15	98.35	0.98	0.96	3	-
GCF_001929375.1	s__Actinomyces oris_B	89.6557	809	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_001937445.1	s__Actinomyces oris_C	89.6215	828	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.06	96.78	0.88	0.86	9	-
GCF_011752065.1	s__Actinomyces sp011752065	89.6008	851	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546825.1	s__Actinomyces oris	89.5939	867	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_900637975.1	s__Actinomyces viscosus	89.5845	879	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001553935.1	s__Actinomyces oris_A	89.2549	846	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.65	97.48	0.94	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:19,279] [INFO] GTDB search result was written to GCF_031296655.1_ASM3129665v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:19,280] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:19,289] [INFO] DFAST_QC result json was written to GCF_031296655.1_ASM3129665v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:19,290] [INFO] DFAST_QC completed!
[2024-01-25 19:48:19,290] [INFO] Total running time: 0h0m59s