[2024-01-24 13:46:00,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:00,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:00,723] [INFO] DQC Reference Directory: /var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference
[2024-01-24 13:46:02,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,012] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgd997f925-5fa6-4431-be6f-415624735ade/GCF_000269805.1_ASM26980v1_genomic.fna.gz | prodigal -d GCF_000269805.1_ASM26980v1_genomic.fna/cds.fna -a GCF_000269805.1_ASM26980v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:11,873] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:11,874] [INFO] Task started: HMMsearch
[2024-01-24 13:46:11,874] [INFO] Running command: hmmsearch --tblout GCF_000269805.1_ASM26980v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference/reference_markers.hmm GCF_000269805.1_ASM26980v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:12,134] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:12,136] [INFO] Found 6/6 markers.
[2024-01-24 13:46:12,169] [INFO] Query marker FASTA was written to GCF_000269805.1_ASM26980v1_genomic.fna/markers.fasta
[2024-01-24 13:46:12,170] [INFO] Task started: Blastn
[2024-01-24 13:46:12,170] [INFO] Running command: blastn -query GCF_000269805.1_ASM26980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference/reference_markers.fasta -out GCF_000269805.1_ASM26980v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:13,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:13,250] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:13,251] [INFO] Target genome list was writen to GCF_000269805.1_ASM26980v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:13,261] [INFO] Task started: fastANI
[2024-01-24 13:46:13,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgd997f925-5fa6-4431-be6f-415624735ade/GCF_000269805.1_ASM26980v1_genomic.fna.gz --refList GCF_000269805.1_ASM26980v1_genomic.fna/target_genomes.txt --output GCF_000269805.1_ASM26980v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:25,942] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:25,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:25,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:25,961] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:25,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:25,961] [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 massiliensis	strain=4401292	GCA_000269805.1	461393	461393	type	True	99.9999	1114	1118	95	conclusive
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	85.5872	821	1118	95	below_threshold
Actinomyces gerencseriae	strain=DSM 6844	GCA_000429265.1	52769	52769	type	True	85.0103	806	1118	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	81.5174	573	1118	95	below_threshold
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	80.5953	489	1118	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	80.4236	455	1118	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.415	444	1118	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	80.3935	477	1118	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	80.3722	495	1118	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.3646	392	1118	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	80.2825	446	1118	95	below_threshold
Actinomyces denticolens	strain=NCTC11490	GCA_900445045.1	52767	52767	type	True	80.2675	463	1118	95	below_threshold
Actinomyces respiraculi	strain=ZJ750	GCA_014595995.2	2744574	2744574	type	True	80.0235	433	1118	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.705	161	1118	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.5057	171	1118	95	below_threshold
Paraoerskovia marina	strain=DSM 21750	GCA_000701465.1	545619	545619	type	True	76.3105	134	1118	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.1057	127	1118	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	75.5724	173	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:25,963] [INFO] DFAST Taxonomy check result was written to GCF_000269805.1_ASM26980v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:25,964] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:25,964] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:25,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference/checkm_data
[2024-01-24 13:46:25,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:26,002] [INFO] Task started: CheckM
[2024-01-24 13:46:26,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000269805.1_ASM26980v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000269805.1_ASM26980v1_genomic.fna/checkm_input GCF_000269805.1_ASM26980v1_genomic.fna/checkm_result
[2024-01-24 13:46:58,361] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:58,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:58,384] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:58,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:58,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000269805.1_ASM26980v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:58,385] [INFO] Task started: Blastn
[2024-01-24 13:46:58,385] [INFO] Running command: blastn -query GCF_000269805.1_ASM26980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefadbf85-85f8-4cde-8088-c043efa78f27/dqc_reference/reference_markers_gtdb.fasta -out GCF_000269805.1_ASM26980v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:59,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:59,976] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:59,976] [INFO] Target genome list was writen to GCF_000269805.1_ASM26980v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:00,007] [INFO] Task started: fastANI
[2024-01-24 13:47:00,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgd997f925-5fa6-4431-be6f-415624735ade/GCF_000269805.1_ASM26980v1_genomic.fna.gz --refList GCF_000269805.1_ASM26980v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000269805.1_ASM26980v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:09,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:09,945] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:09,946] [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_000269805.1	s__Actinomyces massiliensis	99.9999	1114	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.53	98.51	0.94	0.94	3	conclusive
GCA_000711965.1	s__Actinomyces israelii	85.5767	822	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_000429265.1	s__Actinomyces gerencseriae	85.0306	803	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.51	98.51	0.94	0.94	2	-
GCF_000220835.1	s__Actinomyces sp000220835	82.0124	616	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.28	0.97	0.96	3	-
GCF_000429225.1	s__Actinomyces dentalis	81.4486	581	1118	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	81.1332	586	1118	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	80.4283	476	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072185.1	s__Actinomyces denticolens	80.4016	445	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.84	99.40	0.98	0.94	5	-
GCF_001553565.1	s__Actinomyces radicidentis	80.3834	494	1118	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	80.2318	450	1118	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	79.9985	435	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCF_000701465.1	s__Paraoerskovia marina	76.3238	133	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Paraoerskovia	95.0	98.25	98.25	0.95	0.95	2	-
GCF_000718635.1	s__Streptomyces varsoviensis	75.5445	175	1118	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,947] [INFO] GTDB search result was written to GCF_000269805.1_ASM26980v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:09,948] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:09,953] [INFO] DFAST_QC result json was written to GCF_000269805.1_ASM26980v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:09,954] [INFO] DFAST_QC completed!
[2024-01-24 13:47:09,954] [INFO] Total running time: 0h1m9s