[2024-01-24 13:28:11,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,417] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference
[2024-01-24 13:28:12,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:12,634] [INFO] Task started: Prodigal
[2024-01-24 13:28:12,634] [INFO] Running command: gunzip -c /var/lib/cwl/stge3c6f36f-583f-473f-890b-7ad00daa8d54/GCF_000428685.1_ASM42868v1_genomic.fna.gz | prodigal -d GCF_000428685.1_ASM42868v1_genomic.fna/cds.fna -a GCF_000428685.1_ASM42868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:21,823] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:21,823] [INFO] Task started: HMMsearch
[2024-01-24 13:28:21,823] [INFO] Running command: hmmsearch --tblout GCF_000428685.1_ASM42868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference/reference_markers.hmm GCF_000428685.1_ASM42868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:22,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:22,079] [INFO] Found 6/6 markers.
[2024-01-24 13:28:22,109] [INFO] Query marker FASTA was written to GCF_000428685.1_ASM42868v1_genomic.fna/markers.fasta
[2024-01-24 13:28:22,110] [INFO] Task started: Blastn
[2024-01-24 13:28:22,110] [INFO] Running command: blastn -query GCF_000428685.1_ASM42868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference/reference_markers.fasta -out GCF_000428685.1_ASM42868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:23,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:23,194] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:23,194] [INFO] Target genome list was writen to GCF_000428685.1_ASM42868v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:23,333] [INFO] Task started: fastANI
[2024-01-24 13:28:23,334] [INFO] Running command: fastANI --query /var/lib/cwl/stge3c6f36f-583f-473f-890b-7ad00daa8d54/GCF_000428685.1_ASM42868v1_genomic.fna.gz --refList GCF_000428685.1_ASM42868v1_genomic.fna/target_genomes.txt --output GCF_000428685.1_ASM42868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:32,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:32,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:32,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:32,750] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:32,750] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:32,750] [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 slackii	strain=ATCC 49928	GCA_000428685.1	52774	52774	type	True	100.0	1028	1031	95	conclusive
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	99.9874	1029	1031	95	conclusive
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	83.9636	673	1031	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	82.3268	617	1031	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	82.234	631	1031	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	82.1162	603	1031	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	82.0786	605	1031	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	81.4189	503	1031	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_013177295.1	2737173	2737173	type	True	81.4188	473	1031	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	81.3386	443	1031	95	below_threshold
Actinomyces wuliandei	strain=299	GCA_004010955.1	2057743	2057743	type	True	80.5465	503	1031	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.6017	248	1031	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	76.7214	200	1031	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.5499	199	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:32,752] [INFO] DFAST Taxonomy check result was written to GCF_000428685.1_ASM42868v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:32,752] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:32,752] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:32,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference/checkm_data
[2024-01-24 13:28:32,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:32,790] [INFO] Task started: CheckM
[2024-01-24 13:28:32,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428685.1_ASM42868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428685.1_ASM42868v1_genomic.fna/checkm_input GCF_000428685.1_ASM42868v1_genomic.fna/checkm_result
[2024-01-24 13:29:06,441] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:06,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,466] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:06,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:06,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428685.1_ASM42868v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:06,467] [INFO] Task started: Blastn
[2024-01-24 13:29:06,467] [INFO] Running command: blastn -query GCF_000428685.1_ASM42868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fadebfc-cb91-4d85-b555-8ab2f54a931a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428685.1_ASM42868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:08,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:08,116] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:08,116] [INFO] Target genome list was writen to GCF_000428685.1_ASM42868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:08,437] [INFO] Task started: fastANI
[2024-01-24 13:29:08,438] [INFO] Running command: fastANI --query /var/lib/cwl/stge3c6f36f-583f-473f-890b-7ad00daa8d54/GCF_000428685.1_ASM42868v1_genomic.fna.gz --refList GCF_000428685.1_ASM42868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428685.1_ASM42868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:17,070] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:17,090] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:17,090] [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_900637295.1	s__Actinomyces slackii	99.9874	1029	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_013415415.1	s__Actinomyces bowdenii_B	84.1131	593	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	0.98	0.98	2	-
GCF_017592395.1	s__Actinomyces bowdenii	83.9498	674	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.11	99.11	0.96	0.96	2	-
GCF_001929375.1	s__Actinomyces oris_B	82.4789	571	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_011752065.1	s__Actinomyces sp011752065	82.2408	623	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637975.1	s__Actinomyces viscosus	82.2309	631	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001937445.1	s__Actinomyces oris_C	82.1147	586	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.06	96.78	0.88	0.86	9	-
GCF_006546825.1	s__Actinomyces oris	82.0913	604	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_005696555.1	s__Actinomyces oris_E	82.0387	595	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.15	98.35	0.98	0.96	3	-
GCF_900323545.1	s__Actinomyces sp900323545	81.8954	622	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.47	98.47	0.94	0.94	2	-
GCF_002999235.1	s__Actinomyces sp002999235	81.0712	493	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.35	98.35	0.96	0.96	2	-
GCF_004010955.1	s__Actinomyces wuliandei	80.542	503	1031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.68	99.68	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:17,092] [INFO] GTDB search result was written to GCF_000428685.1_ASM42868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:17,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:17,099] [INFO] DFAST_QC result json was written to GCF_000428685.1_ASM42868v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:17,100] [INFO] DFAST_QC completed!
[2024-01-24 13:29:17,100] [INFO] Total running time: 0h1m6s