[2024-01-24 12:23:03,993] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference
[2024-01-24 12:23:05,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,297] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,298] [INFO] Running command: gunzip -c /var/lib/cwl/stg46910a56-2ed8-4eea-99d2-065966841238/GCF_013184985.2_ASM1318498v2_genomic.fna.gz | prodigal -d GCF_013184985.2_ASM1318498v2_genomic.fna/cds.fna -a GCF_013184985.2_ASM1318498v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,658] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,658] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,659] [INFO] Running command: hmmsearch --tblout GCF_013184985.2_ASM1318498v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference/reference_markers.hmm GCF_013184985.2_ASM1318498v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:13,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:13,878] [INFO] Found 6/6 markers.
[2024-01-24 12:23:13,904] [INFO] Query marker FASTA was written to GCF_013184985.2_ASM1318498v2_genomic.fna/markers.fasta
[2024-01-24 12:23:13,904] [INFO] Task started: Blastn
[2024-01-24 12:23:13,904] [INFO] Running command: blastn -query GCF_013184985.2_ASM1318498v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference/reference_markers.fasta -out GCF_013184985.2_ASM1318498v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:15,048] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:15,052] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:15,053] [INFO] Target genome list was writen to GCF_013184985.2_ASM1318498v2_genomic.fna/target_genomes.txt
[2024-01-24 12:23:15,060] [INFO] Task started: fastANI
[2024-01-24 12:23:15,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg46910a56-2ed8-4eea-99d2-065966841238/GCF_013184985.2_ASM1318498v2_genomic.fna.gz --refList GCF_013184985.2_ASM1318498v2_genomic.fna/target_genomes.txt --output GCF_013184985.2_ASM1318498v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:24,058] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:24,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:24,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:24,075] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:24,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:24,075] [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 faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	100.0	900	900	95	conclusive
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	87.2219	664	900	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	81.3839	482	900	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	81.3486	505	900	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	81.2565	466	900	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	81.0623	405	900	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	80.9839	463	900	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	80.8707	494	900	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	80.7341	462	900	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.7092	353	900	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.5358	395	900	95	below_threshold
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	80.305	386	900	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.0504	158	900	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.0378	159	900	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.9063	174	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:24,077] [INFO] DFAST Taxonomy check result was written to GCF_013184985.2_ASM1318498v2_genomic.fna/tc_result.tsv
[2024-01-24 12:23:24,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:24,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:24,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference/checkm_data
[2024-01-24 12:23:24,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:24,115] [INFO] Task started: CheckM
[2024-01-24 12:23:24,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013184985.2_ASM1318498v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013184985.2_ASM1318498v2_genomic.fna/checkm_input GCF_013184985.2_ASM1318498v2_genomic.fna/checkm_result
[2024-01-24 12:23:52,781] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:52,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:52,806] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:52,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:52,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013184985.2_ASM1318498v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:52,808] [INFO] Task started: Blastn
[2024-01-24 12:23:52,808] [INFO] Running command: blastn -query GCF_013184985.2_ASM1318498v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f681755-08e6-4215-b8f0-6e7395f95ca7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013184985.2_ASM1318498v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:54,481] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:54,485] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:54,486] [INFO] Target genome list was writen to GCF_013184985.2_ASM1318498v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:54,493] [INFO] Task started: fastANI
[2024-01-24 12:23:54,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg46910a56-2ed8-4eea-99d2-065966841238/GCF_013184985.2_ASM1318498v2_genomic.fna.gz --refList GCF_013184985.2_ASM1318498v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013184985.2_ASM1318498v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:02,483] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:02,494] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:02,494] [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_013184985.2	s__Actinomyces sp013185035	100.0	900	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.95	0.95	2	conclusive
GCF_000159035.1	s__Actinomyces urogenitalis	87.2411	663	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.08	98.90	0.93	0.88	7	-
GCF_001553565.1	s__Actinomyces radicidentis	81.362	481	900	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	81.3154	505	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCF_000429225.1	s__Actinomyces dentalis	81.2323	468	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCF_000295095.1	s__Actinomyces timonensis	81.0682	404	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278845.1	s__Actinomyces sp001278845	81.0218	464	900	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	80.9561	465	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001929375.1	s__Actinomyces oris_B	80.904	424	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCA_000711965.1	s__Actinomyces israelii	80.8917	492	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_900637165.1	s__Actinomyces howellii	80.8027	473	900	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016598775.1	s__Actinomyces weissii	80.3054	386	900	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 12:24:02,496] [INFO] GTDB search result was written to GCF_013184985.2_ASM1318498v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:02,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:02,502] [INFO] DFAST_QC result json was written to GCF_013184985.2_ASM1318498v2_genomic.fna/dqc_result.json
[2024-01-24 12:24:02,502] [INFO] DFAST_QC completed!
[2024-01-24 12:24:02,503] [INFO] Total running time: 0h0m59s