[2024-01-24 12:52:23,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:23,307] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:23,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference
[2024-01-24 12:52:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:24,522] [INFO] Task started: Prodigal
[2024-01-24 12:52:24,523] [INFO] Running command: gunzip -c /var/lib/cwl/stgf45510e9-f949-4c14-ab8f-bf9c0f9cb5a2/GCF_015711475.1_ASM1571147v2_genomic.fna.gz | prodigal -d GCF_015711475.1_ASM1571147v2_genomic.fna/cds.fna -a GCF_015711475.1_ASM1571147v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:32,477] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:32,477] [INFO] Task started: HMMsearch
[2024-01-24 12:52:32,478] [INFO] Running command: hmmsearch --tblout GCF_015711475.1_ASM1571147v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference/reference_markers.hmm GCF_015711475.1_ASM1571147v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:32,706] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:32,708] [INFO] Found 6/6 markers.
[2024-01-24 12:52:32,733] [INFO] Query marker FASTA was written to GCF_015711475.1_ASM1571147v2_genomic.fna/markers.fasta
[2024-01-24 12:52:32,734] [INFO] Task started: Blastn
[2024-01-24 12:52:32,734] [INFO] Running command: blastn -query GCF_015711475.1_ASM1571147v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference/reference_markers.fasta -out GCF_015711475.1_ASM1571147v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:33,697] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:33,700] [INFO] Selected 19 target genomes.
[2024-01-24 12:52:33,701] [INFO] Target genome list was writen to GCF_015711475.1_ASM1571147v2_genomic.fna/target_genomes.txt
[2024-01-24 12:52:33,762] [INFO] Task started: fastANI
[2024-01-24 12:52:33,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgf45510e9-f949-4c14-ab8f-bf9c0f9cb5a2/GCF_015711475.1_ASM1571147v2_genomic.fna.gz --refList GCF_015711475.1_ASM1571147v2_genomic.fna/target_genomes.txt --output GCF_015711475.1_ASM1571147v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:43,893] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:43,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:43,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:43,908] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:52:43,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:43,909] [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 trachealis	strain=zg-993	GCA_015711475.2	2763540	2763540	type	True	100.0	842	842	95	conclusive
Actinomyces weissii	strain=CCUG 61299	GCA_016598775.1	675090	675090	type	True	84.3177	586	842	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	82.5259	382	842	95	below_threshold
Actinomyces bovis	strain=NCTC11535	GCA_900444995.1	1658	1658	type	True	82.1	560	842	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	79.8891	343	842	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	79.8315	306	842	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	79.7403	360	842	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	79.7131	351	842	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	79.6726	341	842	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	79.6284	334	842	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	79.613	329	842	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	79.591	304	842	95	below_threshold
Actinomyces faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	79.5739	329	842	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287T	GCA_008693165.1	544581	544581	type	True	79.3871	318	842	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287	GCA_006546835.1	544581	544581	type	True	79.37	314	842	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	79.2548	300	842	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.2919	158	842	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.6123	90	842	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.1147	88	842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:43,910] [INFO] DFAST Taxonomy check result was written to GCF_015711475.1_ASM1571147v2_genomic.fna/tc_result.tsv
[2024-01-24 12:52:43,911] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:43,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:43,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference/checkm_data
[2024-01-24 12:52:43,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:43,951] [INFO] Task started: CheckM
[2024-01-24 12:52:43,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015711475.1_ASM1571147v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015711475.1_ASM1571147v2_genomic.fna/checkm_input GCF_015711475.1_ASM1571147v2_genomic.fna/checkm_result
[2024-01-24 12:53:11,663] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:11,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:11,687] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:11,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:11,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015711475.1_ASM1571147v2_genomic.fna/markers.fasta)
[2024-01-24 12:53:11,688] [INFO] Task started: Blastn
[2024-01-24 12:53:11,688] [INFO] Running command: blastn -query GCF_015711475.1_ASM1571147v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3b4f79-b5f2-43f8-83f2-c90ce306723c/dqc_reference/reference_markers_gtdb.fasta -out GCF_015711475.1_ASM1571147v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:13,179] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:13,183] [INFO] Selected 16 target genomes.
[2024-01-24 12:53:13,183] [INFO] Target genome list was writen to GCF_015711475.1_ASM1571147v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:13,250] [INFO] Task started: fastANI
[2024-01-24 12:53:13,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgf45510e9-f949-4c14-ab8f-bf9c0f9cb5a2/GCF_015711475.1_ASM1571147v2_genomic.fna.gz --refList GCF_015711475.1_ASM1571147v2_genomic.fna/target_genomes_gtdb.txt --output GCF_015711475.1_ASM1571147v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:22,064] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:22,085] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:22,085] [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_015711475.1	s__Actinomyces sp015711475	100.0	841	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.54	99.54	0.99	0.99	2	conclusive
GCF_016598775.1	s__Actinomyces weissii	84.3171	586	842	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	82.4582	381	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCA_900444995.1	s__Actinomyces bovis	82.0741	560	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900637975.1	s__Actinomyces viscosus	79.8954	342	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001929375.1	s__Actinomyces oris_B	79.7286	343	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_017592395.1	s__Actinomyces bowdenii	79.7256	361	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.11	99.11	0.96	0.96	2	-
GCF_900103885.1	s__Actinomyces ruminicola	79.707	353	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_001553565.1	s__Actinomyces radicidentis	79.6142	335	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159035.1	s__Actinomyces urogenitalis	79.591	304	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.08	98.90	0.93	0.88	7	-
GCF_013184985.2	s__Actinomyces sp013185035	79.5899	328	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_001937445.1	s__Actinomyces oris_C	79.5506	344	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.06	96.78	0.88	0.86	9	-
GCA_000711965.1	s__Actinomyces israelii	79.4029	357	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_006546835.1	s__Actinomyces johnsonii	79.37	314	842	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.09	97.12	0.94	0.92	6	-
GCF_000195595.1	s__Actinomyces sp000195595	79.3007	316	842	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	79.2704	299	842	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 12:53:22,086] [INFO] GTDB search result was written to GCF_015711475.1_ASM1571147v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:22,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:22,092] [INFO] DFAST_QC result json was written to GCF_015711475.1_ASM1571147v2_genomic.fna/dqc_result.json
[2024-01-24 12:53:22,092] [INFO] DFAST_QC completed!
[2024-01-24 12:53:22,092] [INFO] Total running time: 0h0m59s