[2024-01-24 13:13:08,026] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:08,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:08,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference
[2024-01-24 13:13:09,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:09,253] [INFO] Task started: Prodigal
[2024-01-24 13:13:09,253] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf9b84a3-4454-4f98-8b80-2d8a8b9474e8/GCF_004801905.1_ASM480190v1_genomic.fna.gz | prodigal -d GCF_004801905.1_ASM480190v1_genomic.fna/cds.fna -a GCF_004801905.1_ASM480190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:19,561] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:19,561] [INFO] Task started: HMMsearch
[2024-01-24 13:13:19,561] [INFO] Running command: hmmsearch --tblout GCF_004801905.1_ASM480190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference/reference_markers.hmm GCF_004801905.1_ASM480190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:19,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:19,833] [INFO] Found 6/6 markers.
[2024-01-24 13:13:19,872] [INFO] Query marker FASTA was written to GCF_004801905.1_ASM480190v1_genomic.fna/markers.fasta
[2024-01-24 13:13:19,873] [INFO] Task started: Blastn
[2024-01-24 13:13:19,873] [INFO] Running command: blastn -query GCF_004801905.1_ASM480190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference/reference_markers.fasta -out GCF_004801905.1_ASM480190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:21,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:21,192] [INFO] Selected 29 target genomes.
[2024-01-24 13:13:21,193] [INFO] Target genome list was writen to GCF_004801905.1_ASM480190v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:21,907] [INFO] Task started: fastANI
[2024-01-24 13:13:21,908] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9b84a3-4454-4f98-8b80-2d8a8b9474e8/GCF_004801905.1_ASM480190v1_genomic.fna.gz --refList GCF_004801905.1_ASM480190v1_genomic.fna/target_genomes.txt --output GCF_004801905.1_ASM480190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:42,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:42,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:42,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:42,404] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:42,404] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:42,404] [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
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	79.9529	437	1119	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.9155	516	1119	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	79.896	506	1119	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	79.8645	470	1119	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	79.8236	404	1119	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	79.7607	498	1119	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	79.7078	489	1119	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	79.6736	507	1119	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	79.6128	464	1119	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.5974	477	1119	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	79.5622	481	1119	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	79.5377	329	1119	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	79.494	505	1119	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	79.4341	477	1119	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	79.398	482	1119	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	79.3899	455	1119	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	79.3574	402	1119	95	below_threshold
Microterricola gilva	strain=DSM 18319	GCA_004217495.1	393267	393267	type	True	79.2961	448	1119	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	79.2248	464	1119	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.1953	372	1119	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	79.1946	421	1119	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	79.0732	407	1119	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	79.0135	440	1119	95	below_threshold
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	78.9079	342	1119	95	below_threshold
Labedella phragmitis	strain=11W25H-1	GCA_004078635.1	2498849	2498849	type	True	78.7985	319	1119	95	below_threshold
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	78.7687	322	1119	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	78.6711	305	1119	95	below_threshold
Labedella gwakjiensis	strain=DSM 21548	GCA_003014675.1	390269	390269	type	True	78.5055	335	1119	95	below_threshold
Labedella gwakjiensis	strain=KSW2-17	GCA_003990035.1	390269	390269	type	True	78.4687	341	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:42,406] [INFO] DFAST Taxonomy check result was written to GCF_004801905.1_ASM480190v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:42,406] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:42,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:42,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference/checkm_data
[2024-01-24 13:13:42,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:42,443] [INFO] Task started: CheckM
[2024-01-24 13:13:42,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801905.1_ASM480190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801905.1_ASM480190v1_genomic.fna/checkm_input GCF_004801905.1_ASM480190v1_genomic.fna/checkm_result
[2024-01-24 13:14:17,345] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:17,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:17,365] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:17,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:17,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801905.1_ASM480190v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:17,366] [INFO] Task started: Blastn
[2024-01-24 13:14:17,366] [INFO] Running command: blastn -query GCF_004801905.1_ASM480190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70cf3247-2afc-4598-96d4-8fed78af5d15/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801905.1_ASM480190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:19,267] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:19,270] [INFO] Selected 18 target genomes.
[2024-01-24 13:14:19,270] [INFO] Target genome list was writen to GCF_004801905.1_ASM480190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:19,295] [INFO] Task started: fastANI
[2024-01-24 13:14:19,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf9b84a3-4454-4f98-8b80-2d8a8b9474e8/GCF_004801905.1_ASM480190v1_genomic.fna.gz --refList GCF_004801905.1_ASM480190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801905.1_ASM480190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:33,083] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:33,101] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:33,102] [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_004801905.1	s__Leifsonia_A flavus	100.0	1099	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001422325.1	s__Leifsonia_A sp001422325	80.9652	612	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	96.12	96.12	0.77	0.77	2	-
GCF_004570845.1	s__Leifsonia_A flava	80.8398	623	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	95.29	95.29	0.90	0.90	2	-
GCF_001425325.1	s__Leifsonia_A sp001425325	80.728	604	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008122505.1	s__Agromyces sp008122505	79.9055	517	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104895.1	s__Microterricola viridarii	79.8636	470	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	96.4039	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	79.7189	491	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	79.6783	506	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	79.5691	468	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749395.1	s__Agromyces salentinus	79.4841	506	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	79.4479	513	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	79.4089	490	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797855.1	s__Compostimonas suwonensis	79.3408	428	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217495.1	s__Microterricola gilva	79.3065	447	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	79.2913	434	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006235.1	s__Agromyces sp004006235	79.1546	491	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	79.1215	331	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647635.1	s__Leifsonia xyli_A	79.0828	421	1119	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:33,104] [INFO] GTDB search result was written to GCF_004801905.1_ASM480190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:33,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:33,110] [INFO] DFAST_QC result json was written to GCF_004801905.1_ASM480190v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:33,110] [INFO] DFAST_QC completed!
[2024-01-24 13:14:33,110] [INFO] Total running time: 0h1m25s