[2024-01-24 12:21:57,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference
[2024-01-24 12:21:59,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,613] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a8bf2c1-4096-4d4b-be2a-7a1a48511694/GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/cds.fna -a GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:08,811] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:08,811] [INFO] Task started: HMMsearch
[2024-01-24 12:22:08,812] [INFO] Running command: hmmsearch --tblout GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference/reference_markers.hmm GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:09,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:09,056] [INFO] Found 6/6 markers.
[2024-01-24 12:22:09,085] [INFO] Query marker FASTA was written to GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:09,085] [INFO] Task started: Blastn
[2024-01-24 12:22:09,086] [INFO] Running command: blastn -query GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference/reference_markers.fasta -out GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:10,246] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:10,248] [INFO] Selected 15 target genomes.
[2024-01-24 12:22:10,249] [INFO] Target genome list was writen to GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:10,254] [INFO] Task started: fastANI
[2024-01-24 12:22:10,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8bf2c1-4096-4d4b-be2a-7a1a48511694/GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna.gz --refList GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:22,069] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:22,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:22,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:22,088] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:22,088] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:22,089] [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 ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	100.0	1007	1011	95	conclusive
Actinomyces procaprae	strain=dk561	GCA_004798665.1	2560010	2560010	type	True	88.1138	834	1011	95	below_threshold
Actinomyces succiniciruminis	strain=AM4	GCA_900002405.2	1522002	1522002	type	True	87.6559	786	1011	95	below_threshold
Actinomyces qiguomingii	strain=410	GCA_004102025.1	2057800	2057800	type	True	84.9182	835	1011	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	81.6098	559	1011	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	81.3442	586	1011	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	80.929	513	1011	95	below_threshold
Actinomyces gerencseriae	strain=DSM 6844	GCA_000429265.1	52769	52769	type	True	80.762	538	1011	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.7591	463	1011	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.7232	388	1011	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	80.583	466	1011	95	below_threshold
Actinomyces lilanjuaniae	strain=2129	GCA_003606385.1	2321394	2321394	type	True	79.6119	416	1011	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	76.9552	166	1011	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.6635	184	1011	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	76.0539	244	1011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:22,092] [INFO] DFAST Taxonomy check result was written to GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:22:22,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:22,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:22,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference/checkm_data
[2024-01-24 12:22:22,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:22,133] [INFO] Task started: CheckM
[2024-01-24 12:22:22,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/checkm_input GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:22:54,572] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:54,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:54,596] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:54,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:54,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:22:54,598] [INFO] Task started: Blastn
[2024-01-24 12:22:54,598] [INFO] Running command: blastn -query GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg00843af4-35ac-478a-8c22-2e7b14d00561/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:56,381] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:56,384] [INFO] Selected 6 target genomes.
[2024-01-24 12:22:56,384] [INFO] Target genome list was writen to GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:56,388] [INFO] Task started: fastANI
[2024-01-24 12:22:56,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8bf2c1-4096-4d4b-be2a-7a1a48511694/GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna.gz --refList GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:01,933] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:01,939] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:01,939] [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_900103885.1	s__Actinomyces ruminicola	100.0	1007	1011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	conclusive
GCF_002154335.2	s__Actinomyces sp002154335	89.0645	791	1011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798665.1	s__Actinomyces procaprae	88.1344	832	1011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.28	98.28	0.91	0.91	2	-
GCF_900002405.1	s__Actinomyces succiniciruminis	87.6559	786	1011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.30	98.26	0.87	0.86	3	-
GCF_900098745.1	s__Actinomyces glycerinitolerans	87.4567	840	1011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.41	98.38	0.91	0.91	4	-
GCF_009930875.1	s__Actinomyces sp009930875	86.5678	787	1011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.69	98.69	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:01,943] [INFO] GTDB search result was written to GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:01,943] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:01,946] [INFO] DFAST_QC result json was written to GCF_900103885.1_IMG-taxon_2651870319_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:23:01,946] [INFO] DFAST_QC completed!
[2024-01-24 12:23:01,946] [INFO] Total running time: 0h1m4s