[2024-01-24 13:16:56,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference
[2024-01-24 13:16:57,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,408] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ed59629-14f3-42d0-8d7e-5908a55154ab/GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna.gz | prodigal -d GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/cds.fna -a GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:05,618] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:05,619] [INFO] Task started: HMMsearch
[2024-01-24 13:17:05,619] [INFO] Running command: hmmsearch --tblout GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference/reference_markers.hmm GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:05,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:05,855] [INFO] Found 6/6 markers.
[2024-01-24 13:17:05,894] [INFO] Query marker FASTA was written to GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/markers.fasta
[2024-01-24 13:17:05,894] [INFO] Task started: Blastn
[2024-01-24 13:17:05,894] [INFO] Running command: blastn -query GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference/reference_markers.fasta -out GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:06,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:06,563] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:06,563] [INFO] Target genome list was writen to GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 13:17:06,573] [INFO] Task started: fastANI
[2024-01-24 13:17:06,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed59629-14f3-42d0-8d7e-5908a55154ab/GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna.gz --refList GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/target_genomes.txt --output GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:19,723] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:19,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:19,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:19,737] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:19,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:19,738] [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
Flaviflexus massiliensis	strain=SIT4	GCA_001375495.1	1522309	1522309	type	True	100.0	873	875	95	conclusive
Flaviflexus ciconiae	strain=H23T48	GCA_003971195.1	2496867	2496867	type	True	80.004	408	875	95	below_threshold
Flaviflexus equikiangi	strain=dk850	GCA_014069875.1	2758573	2758573	type	True	78.9203	292	875	95	below_threshold
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	78.3989	298	875	95	below_threshold
Flaviflexus huanghaiensis	strain=CICC 10486	GCA_014118685.1	1111473	1111473	type	True	78.1501	209	875	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	77.4419	80	875	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	77.3691	76	875	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.3179	87	875	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	77.2182	75	875	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	77.0009	74	875	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	76.931	59	875	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	76.7359	67	875	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	76.6226	61	875	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	76.5699	78	875	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	76.0967	51	875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:19,739] [INFO] DFAST Taxonomy check result was written to GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 13:17:19,740] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:19,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:19,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference/checkm_data
[2024-01-24 13:17:19,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:19,774] [INFO] Task started: CheckM
[2024-01-24 13:17:19,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/checkm_input GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/checkm_result
[2024-01-24 13:17:49,093] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:49,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:49,107] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:49,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:49,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 13:17:49,108] [INFO] Task started: Blastn
[2024-01-24 13:17:49,108] [INFO] Running command: blastn -query GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f084a5d-4d55-4486-910b-a829d135c536/dqc_reference/reference_markers_gtdb.fasta -out GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:50,103] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:50,107] [INFO] Selected 20 target genomes.
[2024-01-24 13:17:50,108] [INFO] Target genome list was writen to GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:50,122] [INFO] Task started: fastANI
[2024-01-24 13:17:50,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ed59629-14f3-42d0-8d7e-5908a55154ab/GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna.gz --refList GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:01,972] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:01,983] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:01,983] [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_001375495.1	s__Flaviflexus massiliensis	100.0	873	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003971195.1	s__Flaviflexus sp003971195	80.0375	405	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014069875.1	s__Flaviflexus sp014069875	78.9665	293	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	99.13	99.13	0.93	0.93	3	-
GCF_003952265.1	s__Flaviflexus salsibiostraticola	78.3886	298	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014118685.1	s__Flaviflexus huanghaiensis	78.1501	209	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469025.1	s__Trueperella bernardiae	77.3206	84	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCF_006546825.1	s__Actinomyces oris	77.2233	74	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_003814705.1	s__Georgenia muralis	77.2048	76	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900499005.1	s__Pauljensenia culturomici	77.0228	63	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595995.2	s__Actinomyces sp011751985	76.8582	70	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.79	99.58	0.98	0.98	3	-
GCF_006716205.1	s__Oryzihumus leptocrescens	76.83	55	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193175.1	s__Georgenia ruanii	76.5683	78	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696205.1	s__Cellulomonas sp003696205	76.3731	62	875	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,988] [INFO] GTDB search result was written to GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:01,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:01,994] [INFO] DFAST_QC result json was written to GCF_001375495.1_Flaviflexus_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 13:18:01,994] [INFO] DFAST_QC completed!
[2024-01-24 13:18:01,994] [INFO] Total running time: 0h1m6s