[2024-01-24 14:20:14,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference
[2024-01-24 14:20:15,514] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,515] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg692479b3-fd2f-44ea-aa2b-eed70d93f211/GCF_004102025.1_ASM410202v1_genomic.fna.gz | prodigal -d GCF_004102025.1_ASM410202v1_genomic.fna/cds.fna -a GCF_004102025.1_ASM410202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:28,927] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:28,927] [INFO] Task started: HMMsearch
[2024-01-24 14:20:28,927] [INFO] Running command: hmmsearch --tblout GCF_004102025.1_ASM410202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference/reference_markers.hmm GCF_004102025.1_ASM410202v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:29,223] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:29,225] [INFO] Found 6/6 markers.
[2024-01-24 14:20:29,261] [INFO] Query marker FASTA was written to GCF_004102025.1_ASM410202v1_genomic.fna/markers.fasta
[2024-01-24 14:20:29,261] [INFO] Task started: Blastn
[2024-01-24 14:20:29,261] [INFO] Running command: blastn -query GCF_004102025.1_ASM410202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference/reference_markers.fasta -out GCF_004102025.1_ASM410202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:30,367] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:30,372] [INFO] Selected 16 target genomes.
[2024-01-24 14:20:30,373] [INFO] Target genome list was writen to GCF_004102025.1_ASM410202v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:30,398] [INFO] Task started: fastANI
[2024-01-24 14:20:30,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg692479b3-fd2f-44ea-aa2b-eed70d93f211/GCF_004102025.1_ASM410202v1_genomic.fna.gz --refList GCF_004102025.1_ASM410202v1_genomic.fna/target_genomes.txt --output GCF_004102025.1_ASM410202v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:42,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:42,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:42,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:43,003] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:43,003] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:43,004] [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 qiguomingii	strain=410	GCA_004102025.1	2057800	2057800	type	True	100.0	1324	1329	95	conclusive
Actinomyces succiniciruminis	strain=AM4	GCA_900002405.2	1522002	1522002	type	True	85.4272	800	1329	95	below_threshold
Actinomyces procaprae	strain=dk561	GCA_004798665.1	2560010	2560010	type	True	84.9938	909	1329	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	84.8528	833	1329	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	80.0067	490	1329	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	79.9056	544	1329	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	79.6868	388	1329	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	79.6014	424	1329	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	79.5999	344	1329	95	below_threshold
Actinomyces lilanjuaniae	strain=2129	GCA_003606385.1	2321394	2321394	type	True	78.8776	359	1329	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	76.9575	230	1329	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.8186	138	1329	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	76.7253	104	1329	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	76.4601	117	1329	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	76.2584	72	1329	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	76.0521	147	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:43,005] [INFO] DFAST Taxonomy check result was written to GCF_004102025.1_ASM410202v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:43,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:43,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:43,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference/checkm_data
[2024-01-24 14:20:43,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:43,051] [INFO] Task started: CheckM
[2024-01-24 14:20:43,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004102025.1_ASM410202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004102025.1_ASM410202v1_genomic.fna/checkm_input GCF_004102025.1_ASM410202v1_genomic.fna/checkm_result
[2024-01-24 14:21:23,470] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:23,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:23,494] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:23,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:23,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004102025.1_ASM410202v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:23,495] [INFO] Task started: Blastn
[2024-01-24 14:21:23,495] [INFO] Running command: blastn -query GCF_004102025.1_ASM410202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeed7333c-64ea-44cf-a318-702f2949c26c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004102025.1_ASM410202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:25,029] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:25,033] [INFO] Selected 8 target genomes.
[2024-01-24 14:21:25,033] [INFO] Target genome list was writen to GCF_004102025.1_ASM410202v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:25,058] [INFO] Task started: fastANI
[2024-01-24 14:21:25,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg692479b3-fd2f-44ea-aa2b-eed70d93f211/GCF_004102025.1_ASM410202v1_genomic.fna.gz --refList GCF_004102025.1_ASM410202v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004102025.1_ASM410202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:33,564] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:33,575] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:33,575] [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_004102025.1	s__Actinomyces qiguomingii	100.0	1324	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.95	99.95	1.00	1.00	2	conclusive
GCF_009930875.1	s__Actinomyces sp009930875	85.67	803	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.69	98.69	0.97	0.97	2	-
GCF_900002405.1	s__Actinomyces succiniciruminis	85.4165	801	1329	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	85.3746	907	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	96.3414	98.41	98.38	0.91	0.91	4	-
GCF_004798665.1	s__Actinomyces procaprae	85.0108	907	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.28	98.28	0.91	0.91	2	-
GCF_900103885.1	s__Actinomyces ruminicola	84.8511	833	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_002154335.2	s__Actinomyces sp002154335	84.7276	818	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193175.1	s__Georgenia ruanii	76.9273	233	1329	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:33,577] [INFO] GTDB search result was written to GCF_004102025.1_ASM410202v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:33,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:33,581] [INFO] DFAST_QC result json was written to GCF_004102025.1_ASM410202v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:33,582] [INFO] DFAST_QC completed!
[2024-01-24 14:21:33,582] [INFO] Total running time: 0h1m19s