[2024-01-24 12:30:09,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:09,214] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:09,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference
[2024-01-24 12:30:12,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:12,008] [INFO] Task started: Prodigal
[2024-01-24 12:30:12,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg21a9480a-951e-426b-bcb9-74b2ecef3330/GCF_014595995.2_ASM1459599v2_genomic.fna.gz | prodigal -d GCF_014595995.2_ASM1459599v2_genomic.fna/cds.fna -a GCF_014595995.2_ASM1459599v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:20,707] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:20,708] [INFO] Task started: HMMsearch
[2024-01-24 12:30:20,708] [INFO] Running command: hmmsearch --tblout GCF_014595995.2_ASM1459599v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference/reference_markers.hmm GCF_014595995.2_ASM1459599v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:20,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:20,949] [INFO] Found 6/6 markers.
[2024-01-24 12:30:20,972] [INFO] Query marker FASTA was written to GCF_014595995.2_ASM1459599v2_genomic.fna/markers.fasta
[2024-01-24 12:30:20,973] [INFO] Task started: Blastn
[2024-01-24 12:30:20,973] [INFO] Running command: blastn -query GCF_014595995.2_ASM1459599v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference/reference_markers.fasta -out GCF_014595995.2_ASM1459599v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:22,086] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:22,090] [INFO] Selected 18 target genomes.
[2024-01-24 12:30:22,090] [INFO] Target genome list was writen to GCF_014595995.2_ASM1459599v2_genomic.fna/target_genomes.txt
[2024-01-24 12:30:22,099] [INFO] Task started: fastANI
[2024-01-24 12:30:22,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a9480a-951e-426b-bcb9-74b2ecef3330/GCF_014595995.2_ASM1459599v2_genomic.fna.gz --refList GCF_014595995.2_ASM1459599v2_genomic.fna/target_genomes.txt --output GCF_014595995.2_ASM1459599v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:33,695] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:33,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:33,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:33,710] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:33,711] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:33,711] [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 respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	100.0	970	970	95	conclusive
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	82.1334	550	970	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	81.8478	439	970	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	81.7437	542	970	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	81.7339	489	970	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	81.5181	458	970	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	81.4985	484	970	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	81.2854	502	970	95	below_threshold
Actinomyces faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	81.2599	519	970	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	81.2523	500	970	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	81.2267	516	970	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	80.9724	487	970	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	80.8945	490	970	95	below_threshold
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	80.535	408	970	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.0998	301	970	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	77.6859	333	970	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.9548	198	970	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.6636	239	970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:33,712] [INFO] DFAST Taxonomy check result was written to GCF_014595995.2_ASM1459599v2_genomic.fna/tc_result.tsv
[2024-01-24 12:30:33,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:33,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:33,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference/checkm_data
[2024-01-24 12:30:33,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:33,748] [INFO] Task started: CheckM
[2024-01-24 12:30:33,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014595995.2_ASM1459599v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014595995.2_ASM1459599v2_genomic.fna/checkm_input GCF_014595995.2_ASM1459599v2_genomic.fna/checkm_result
[2024-01-24 12:31:12,044] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:12,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:12,065] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:12,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:12,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014595995.2_ASM1459599v2_genomic.fna/markers.fasta)
[2024-01-24 12:31:12,066] [INFO] Task started: Blastn
[2024-01-24 12:31:12,067] [INFO] Running command: blastn -query GCF_014595995.2_ASM1459599v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b05a45-1f03-401c-8e7c-e674f786074f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014595995.2_ASM1459599v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:13,983] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:13,987] [INFO] Selected 16 target genomes.
[2024-01-24 12:31:13,987] [INFO] Target genome list was writen to GCF_014595995.2_ASM1459599v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:13,999] [INFO] Task started: fastANI
[2024-01-24 12:31:13,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg21a9480a-951e-426b-bcb9-74b2ecef3330/GCF_014595995.2_ASM1459599v2_genomic.fna.gz --refList GCF_014595995.2_ASM1459599v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014595995.2_ASM1459599v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:26,078] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:26,092] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:26,092] [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_014595995.2	s__Actinomyces sp011751985	100.0	970	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	conclusive
GCF_001553565.1	s__Actinomyces radicidentis	82.1254	553	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355765.1	s__Actinomyces haliotis	81.7688	486	970	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	81.7369	544	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_001278845.1	s__Actinomyces sp001278845	81.5065	537	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295095.1	s__Actinomyces timonensis	81.4414	488	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637165.1	s__Actinomyces howellii	81.3367	519	970	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	81.2721	518	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_900637975.1	s__Actinomyces viscosus	81.2188	514	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000711965.1	s__Actinomyces israelii	81.1872	542	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_900103885.1	s__Actinomyces ruminicola	80.9968	506	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_000159035.1	s__Actinomyces urogenitalis	80.9591	488	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.08	98.90	0.93	0.88	7	-
GCF_017592395.1	s__Actinomyces bowdenii	80.882	491	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.11	99.11	0.96	0.96	2	-
GCF_900098745.1	s__Actinomyces glycerinitolerans	80.5945	497	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.41	98.38	0.91	0.91	4	-
GCF_016598775.1	s__Actinomyces weissii	80.5293	406	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002999235.1	s__Actinomyces sp002999235	80.3854	428	970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.35	98.35	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:26,094] [INFO] GTDB search result was written to GCF_014595995.2_ASM1459599v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:26,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:26,099] [INFO] DFAST_QC result json was written to GCF_014595995.2_ASM1459599v2_genomic.fna/dqc_result.json
[2024-01-24 12:31:26,099] [INFO] DFAST_QC completed!
[2024-01-24 12:31:26,099] [INFO] Total running time: 0h1m17s