[2024-01-24 14:55:08,756] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,758] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference
[2024-01-24 14:55:10,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,275] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa8c59a9-7751-4188-81dd-bf7283194bbe/GCF_015355765.1_ASM1535576v1_genomic.fna.gz | prodigal -d GCF_015355765.1_ASM1535576v1_genomic.fna/cds.fna -a GCF_015355765.1_ASM1535576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:17,020] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:17,021] [INFO] Task started: HMMsearch
[2024-01-24 14:55:17,021] [INFO] Running command: hmmsearch --tblout GCF_015355765.1_ASM1535576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference/reference_markers.hmm GCF_015355765.1_ASM1535576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:17,264] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:17,266] [INFO] Found 6/6 markers.
[2024-01-24 14:55:17,297] [INFO] Query marker FASTA was written to GCF_015355765.1_ASM1535576v1_genomic.fna/markers.fasta
[2024-01-24 14:55:17,298] [INFO] Task started: Blastn
[2024-01-24 14:55:17,298] [INFO] Running command: blastn -query GCF_015355765.1_ASM1535576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference/reference_markers.fasta -out GCF_015355765.1_ASM1535576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:18,459] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:18,463] [INFO] Selected 19 target genomes.
[2024-01-24 14:55:18,464] [INFO] Target genome list was writen to GCF_015355765.1_ASM1535576v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:18,491] [INFO] Task started: fastANI
[2024-01-24 14:55:18,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8c59a9-7751-4188-81dd-bf7283194bbe/GCF_015355765.1_ASM1535576v1_genomic.fna.gz --refList GCF_015355765.1_ASM1535576v1_genomic.fna/target_genomes.txt --output GCF_015355765.1_ASM1535576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:30,925] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:30,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:30,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:30,941] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:30,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:30,942] [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 haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	100.0	871	873	95	conclusive
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	90.1986	766	873	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	81.8256	480	873	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	81.7193	521	873	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	81.4462	417	873	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	81.4248	543	873	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	81.3621	477	873	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	81.3198	470	873	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	81.1714	485	873	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	81.1069	524	873	95	below_threshold
Actinomyces howellii	strain=NCTC11636	GCA_900637165.1	52771	52771	type	True	81.024	512	873	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	81.0135	515	873	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	80.9794	501	873	95	below_threshold
Actinomyces gerencseriae	strain=DSM 6844	GCA_000429265.1	52769	52769	type	True	80.7699	486	873	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	80.5739	462	873	95	below_threshold
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	79.8213	347	873	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.8729	276	873	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.8316	322	873	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.8301	271	873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:30,945] [INFO] DFAST Taxonomy check result was written to GCF_015355765.1_ASM1535576v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:30,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:30,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:30,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference/checkm_data
[2024-01-24 14:55:30,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:30,979] [INFO] Task started: CheckM
[2024-01-24 14:55:30,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015355765.1_ASM1535576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015355765.1_ASM1535576v1_genomic.fna/checkm_input GCF_015355765.1_ASM1535576v1_genomic.fna/checkm_result
[2024-01-24 14:56:07,360] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:07,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:07,376] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:07,377] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:07,377] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015355765.1_ASM1535576v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:07,377] [INFO] Task started: Blastn
[2024-01-24 14:56:07,378] [INFO] Running command: blastn -query GCF_015355765.1_ASM1535576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg163c92c8-b87b-4496-b3f2-aa3e7756b13c/dqc_reference/reference_markers_gtdb.fasta -out GCF_015355765.1_ASM1535576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:09,253] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:09,257] [INFO] Selected 14 target genomes.
[2024-01-24 14:56:09,257] [INFO] Target genome list was writen to GCF_015355765.1_ASM1535576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:09,271] [INFO] Task started: fastANI
[2024-01-24 14:56:09,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8c59a9-7751-4188-81dd-bf7283194bbe/GCF_015355765.1_ASM1535576v1_genomic.fna.gz --refList GCF_015355765.1_ASM1535576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015355765.1_ASM1535576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:18,885] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:18,904] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:18,904] [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_015355765.1	s__Actinomyces haliotis	100.0	871	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001553565.1	s__Actinomyces radicidentis	90.2014	767	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595995.2	s__Actinomyces sp011751985	81.7812	483	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCF_000295095.1	s__Actinomyces timonensis	81.7329	520	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429225.1	s__Actinomyces dentalis	81.3794	546	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_011752065.1	s__Actinomyces sp011752065	81.2296	489	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000711965.1	s__Actinomyces israelii	81.1318	522	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_001929375.1	s__Actinomyces oris_B	81.0923	464	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_900637165.1	s__Actinomyces howellii	81.0103	513	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900637975.1	s__Actinomyces viscosus	80.9924	499	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013184985.2	s__Actinomyces sp013185035	80.9535	445	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_000429265.1	s__Actinomyces gerencseriae	80.7572	487	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.51	98.51	0.94	0.94	2	-
GCF_900103885.1	s__Actinomyces ruminicola	80.5207	467	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_016598775.1	s__Actinomyces weissii	79.8369	346	873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:18,905] [INFO] GTDB search result was written to GCF_015355765.1_ASM1535576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:18,906] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:18,910] [INFO] DFAST_QC result json was written to GCF_015355765.1_ASM1535576v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:18,910] [INFO] DFAST_QC completed!
[2024-01-24 14:56:18,911] [INFO] Total running time: 0h1m10s