[2024-01-24 14:53:50,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,246] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference
[2024-01-24 14:53:51,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,457] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,457] [INFO] Running command: gunzip -c /var/lib/cwl/stg85e18dcf-814f-44db-b482-9bfc5855359d/GCF_030811095.1_ASM3081109v1_genomic.fna.gz | prodigal -d GCF_030811095.1_ASM3081109v1_genomic.fna/cds.fna -a GCF_030811095.1_ASM3081109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:53:58,861] [INFO] Task succeeded: Prodigal
[2024-01-24 14:53:58,862] [INFO] Task started: HMMsearch
[2024-01-24 14:53:58,862] [INFO] Running command: hmmsearch --tblout GCF_030811095.1_ASM3081109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference/reference_markers.hmm GCF_030811095.1_ASM3081109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:53:59,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:53:59,104] [INFO] Found 6/6 markers.
[2024-01-24 14:53:59,131] [INFO] Query marker FASTA was written to GCF_030811095.1_ASM3081109v1_genomic.fna/markers.fasta
[2024-01-24 14:53:59,131] [INFO] Task started: Blastn
[2024-01-24 14:53:59,131] [INFO] Running command: blastn -query GCF_030811095.1_ASM3081109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference/reference_markers.fasta -out GCF_030811095.1_ASM3081109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:00,010] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:00,014] [INFO] Selected 21 target genomes.
[2024-01-24 14:54:00,015] [INFO] Target genome list was writen to GCF_030811095.1_ASM3081109v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:00,035] [INFO] Task started: fastANI
[2024-01-24 14:54:00,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg85e18dcf-814f-44db-b482-9bfc5855359d/GCF_030811095.1_ASM3081109v1_genomic.fna.gz --refList GCF_030811095.1_ASM3081109v1_genomic.fna/target_genomes.txt --output GCF_030811095.1_ASM3081109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:11,900] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:11,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:11,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:11,922] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:54:11,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:54:11,923] [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
Trueperella bernardiae	strain=LCDC 89-0504	GCA_001469025.1	59561	59561	type	True	85.2641	570	815	95	below_threshold
Trueperella pecoris	strain=19M2397	GCA_014926385.1	2733571	2733571	type	True	79.9921	353	815	95	below_threshold
Trueperella pyogenes	strain=DSM 20630	GCA_014191445.1	1661	1661	type	True	79.9416	336	815	95	below_threshold
Trueperella pyogenes	strain=NCTC5224	GCA_900460345.1	1661	1661	type	True	79.9292	362	815	95	below_threshold
Trueperella bialowiezensis	strain=NCTC13354	GCA_900637955.1	312285	312285	type	True	77.9959	193	815	95	below_threshold
Actinomyces faecalis	strain=ZJ34	GCA_013184985.2	2722820	2722820	type	True	77.297	102	815	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	77.2432	144	815	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	77.1566	172	815	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.9747	150	815	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	76.9061	103	815	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	76.8415	118	815	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	76.709	61	815	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	76.7072	100	815	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	76.5575	110	815	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.4583	83	815	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.355	131	815	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	76.2016	124	815	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	76.1362	89	815	95	below_threshold
Gryllotalpicola ginsengisoli	strain=DSM 22003	GCA_000419445.1	444608	444608	type	True	76.0784	76	815	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	75.932	75	815	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	75.6838	52	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:11,924] [INFO] DFAST Taxonomy check result was written to GCF_030811095.1_ASM3081109v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:11,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:11,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:11,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference/checkm_data
[2024-01-24 14:54:11,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:11,951] [INFO] Task started: CheckM
[2024-01-24 14:54:11,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811095.1_ASM3081109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811095.1_ASM3081109v1_genomic.fna/checkm_input GCF_030811095.1_ASM3081109v1_genomic.fna/checkm_result
[2024-01-24 14:54:38,535] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:38,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:38,557] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:38,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:38,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811095.1_ASM3081109v1_genomic.fna/markers.fasta)
[2024-01-24 14:54:38,558] [INFO] Task started: Blastn
[2024-01-24 14:54:38,558] [INFO] Running command: blastn -query GCF_030811095.1_ASM3081109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf19d3803-0cbd-4056-be94-93f33245d907/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811095.1_ASM3081109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:39,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:39,870] [INFO] Selected 20 target genomes.
[2024-01-24 14:54:39,871] [INFO] Target genome list was writen to GCF_030811095.1_ASM3081109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:39,895] [INFO] Task started: fastANI
[2024-01-24 14:54:39,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg85e18dcf-814f-44db-b482-9bfc5855359d/GCF_030811095.1_ASM3081109v1_genomic.fna.gz --refList GCF_030811095.1_ASM3081109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811095.1_ASM3081109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:54:51,794] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:51,814] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:54:51,815] [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_001469025.1	s__Trueperella bernardiae	85.245	571	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCF_014926385.1	s__Trueperella pecoris	79.9804	354	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	97.88	95.38	0.92	0.88	4	-
GCF_900460345.1	s__Trueperella pyogenes	79.9495	364	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	98.61	97.91	0.94	0.87	20	-
GCF_900637955.1	s__Trueperella bialowiezensis	77.9193	192	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466165.1	s__Peptidiphaga sp000466165	77.4702	126	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Peptidiphaga	95.0	99.10	98.96	0.93	0.91	3	-
GCF_003952265.1	s__Flaviflexus salsibiostraticola	77.3144	134	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184985.2	s__Actinomyces sp013185035	77.297	102	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.31	99.31	0.95	0.95	2	-
GCF_003814705.1	s__Georgenia muralis	77.1567	142	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553565.1	s__Actinomyces radicidentis	77.0981	170	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193185.1	s__Georgenia thermotolerans	77.0535	171	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900163555.1	s__JB111 sp900163555	76.9129	137	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__JB111	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388445.1	s__Cellulomonas sp018388445	76.8684	118	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCF_006546825.1	s__Actinomyces oris	76.8293	126	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_014204755.1	s__Brachybacterium aquaticum	76.821	119	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135385.1	s__Xylanimonas sp004135385	76.6668	132	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	76.4035	99	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_003202285.1	s__Saccharomonospora muralis	76.1038	91	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003594885.1	s__Vallicoccus soli	75.9434	96	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Vallicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873635.1	s__Nocardioides sp014873635	75.7828	88	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	75.6435	54	815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:54:51,816] [INFO] GTDB search result was written to GCF_030811095.1_ASM3081109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:54:51,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:54:51,825] [INFO] DFAST_QC result json was written to GCF_030811095.1_ASM3081109v1_genomic.fna/dqc_result.json
[2024-01-24 14:54:51,825] [INFO] DFAST_QC completed!
[2024-01-24 14:54:51,825] [INFO] Total running time: 0h1m2s