[2024-01-24 12:22:37,754] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,757] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,757] [INFO] DQC Reference Directory: /var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference
[2024-01-24 12:22:39,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,118] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg91128e67-b3b2-4df0-ad36-e02e1771628a/GCF_004104015.1_ASM410401v1_genomic.fna.gz | prodigal -d GCF_004104015.1_ASM410401v1_genomic.fna/cds.fna -a GCF_004104015.1_ASM410401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:47,903] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:47,903] [INFO] Task started: HMMsearch
[2024-01-24 12:22:47,903] [INFO] Running command: hmmsearch --tblout GCF_004104015.1_ASM410401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference/reference_markers.hmm GCF_004104015.1_ASM410401v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:48,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:48,157] [INFO] Found 6/6 markers.
[2024-01-24 12:22:48,184] [INFO] Query marker FASTA was written to GCF_004104015.1_ASM410401v1_genomic.fna/markers.fasta
[2024-01-24 12:22:48,184] [INFO] Task started: Blastn
[2024-01-24 12:22:48,184] [INFO] Running command: blastn -query GCF_004104015.1_ASM410401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference/reference_markers.fasta -out GCF_004104015.1_ASM410401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:49,200] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:49,206] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:49,207] [INFO] Target genome list was writen to GCF_004104015.1_ASM410401v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:49,227] [INFO] Task started: fastANI
[2024-01-24 12:22:49,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg91128e67-b3b2-4df0-ad36-e02e1771628a/GCF_004104015.1_ASM410401v1_genomic.fna.gz --refList GCF_004104015.1_ASM410401v1_genomic.fna/target_genomes.txt --output GCF_004104015.1_ASM410401v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:59,887] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:59,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:59,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:59,907] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:59,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:59,907] [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 oricola	strain=R5292	GCA_004104015.1	206043	206043	type	True	100.0	938	941	95	conclusive
Actinomyces bowdenii	strain=DSM 15435	GCA_017592395.1	131109	131109	type	True	80.8778	494	941	95	below_threshold
Actinomyces slackii	strain=ATCC 49928	GCA_000428685.1	52774	52774	type	True	80.6325	492	941	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	80.5833	513	941	95	below_threshold
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	80.5141	500	941	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	80.423	431	941	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	80.1904	416	941	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.0687	379	941	95	below_threshold
Actinomyces denticolens	strain=NCTC11490	GCA_900445045.1	52767	52767	type	True	80.0645	435	941	95	below_threshold
Actinomyces gaoshouyii	strain=pika_113	GCA_002072175.1	1960083	1960083	type	True	80.0638	387	941	95	below_threshold
Actinomyces gaoshouyii	strain=CGMCC 4.7372	GCA_014646495.1	1960083	1960083	type	True	80.0531	394	941	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	79.9545	458	941	95	below_threshold
Actinomyces howellii	strain=NCTC11636	GCA_900637165.1	52771	52771	type	True	79.8411	453	941	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	79.8255	445	941	95	below_threshold
Actinomyces gerencseriae	strain=DSM 6844	GCA_000429265.1	52769	52769	type	True	79.6741	448	941	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	79.5315	371	941	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.2725	191	941	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	76.5292	91	941	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.4471	110	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:59,909] [INFO] DFAST Taxonomy check result was written to GCF_004104015.1_ASM410401v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:59,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:59,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:59,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference/checkm_data
[2024-01-24 12:22:59,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:59,944] [INFO] Task started: CheckM
[2024-01-24 12:22:59,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004104015.1_ASM410401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004104015.1_ASM410401v1_genomic.fna/checkm_input GCF_004104015.1_ASM410401v1_genomic.fna/checkm_result
[2024-01-24 12:23:29,735] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:29,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,758] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:29,758] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:29,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004104015.1_ASM410401v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:29,759] [INFO] Task started: Blastn
[2024-01-24 12:23:29,759] [INFO] Running command: blastn -query GCF_004104015.1_ASM410401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebfb9366-ec51-4b81-b104-d95f003d76de/dqc_reference/reference_markers_gtdb.fasta -out GCF_004104015.1_ASM410401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:31,187] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:31,191] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:31,192] [INFO] Target genome list was writen to GCF_004104015.1_ASM410401v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:31,216] [INFO] Task started: fastANI
[2024-01-24 12:23:31,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg91128e67-b3b2-4df0-ad36-e02e1771628a/GCF_004104015.1_ASM410401v1_genomic.fna.gz --refList GCF_004104015.1_ASM410401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004104015.1_ASM410401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:41,387] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:41,405] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:41,406] [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_004104015.1	s__Actinomyces oricola	100.0	938	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002999235.1	s__Actinomyces sp002999235	81.1142	485	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.35	98.35	0.96	0.96	2	-
GCF_013415415.1	s__Actinomyces bowdenii_B	80.9127	428	941	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	80.8656	495	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.11	99.11	0.96	0.96	2	-
GCF_000429225.1	s__Actinomyces dentalis	80.6512	499	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	98.22	0.92	0.92	2	-
GCA_000711965.1	s__Actinomyces israelii	80.6025	511	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.26	99.26	0.94	0.94	2	-
GCF_001929375.1	s__Actinomyces oris_B	80.5784	456	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_900637295.1	s__Actinomyces slackii	80.4921	503	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000295095.1	s__Actinomyces timonensis	80.446	429	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278845.1	s__Actinomyces sp001278845	80.4363	511	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195595.1	s__Actinomyces sp000195595	80.213	442	941	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	80.1767	417	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.84	99.40	0.98	0.94	5	-
GCF_002072175.1	s__Actinomyces gaoshouyii	80.0494	388	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.77	99.54	0.99	0.99	3	-
GCF_900103885.1	s__Actinomyces ruminicola	79.9531	458	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
GCF_900637165.1	s__Actinomyces howellii	79.8411	453	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220835.1	s__Actinomyces sp000220835	79.3054	389	941	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.28	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:41,407] [INFO] GTDB search result was written to GCF_004104015.1_ASM410401v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:41,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:41,412] [INFO] DFAST_QC result json was written to GCF_004104015.1_ASM410401v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:41,413] [INFO] DFAST_QC completed!
[2024-01-24 12:23:41,413] [INFO] Total running time: 0h1m4s