[2024-01-24 14:55:50,890] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:50,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:50,893] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference
[2024-01-24 14:55:52,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,154] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,154] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf4d720c-58a3-489e-b2a5-cdb8fe1801d6/GCF_002216795.1_ASM221679v1_genomic.fna.gz | prodigal -d GCF_002216795.1_ASM221679v1_genomic.fna/cds.fna -a GCF_002216795.1_ASM221679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:02,621] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:02,622] [INFO] Task started: HMMsearch
[2024-01-24 14:56:02,622] [INFO] Running command: hmmsearch --tblout GCF_002216795.1_ASM221679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference/reference_markers.hmm GCF_002216795.1_ASM221679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:02,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:02,888] [INFO] Found 6/6 markers.
[2024-01-24 14:56:02,926] [INFO] Query marker FASTA was written to GCF_002216795.1_ASM221679v1_genomic.fna/markers.fasta
[2024-01-24 14:56:02,926] [INFO] Task started: Blastn
[2024-01-24 14:56:02,926] [INFO] Running command: blastn -query GCF_002216795.1_ASM221679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference/reference_markers.fasta -out GCF_002216795.1_ASM221679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:04,105] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:04,107] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:04,108] [INFO] Target genome list was writen to GCF_002216795.1_ASM221679v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:04,127] [INFO] Task started: fastANI
[2024-01-24 14:56:04,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf4d720c-58a3-489e-b2a5-cdb8fe1801d6/GCF_002216795.1_ASM221679v1_genomic.fna.gz --refList GCF_002216795.1_ASM221679v1_genomic.fna/target_genomes.txt --output GCF_002216795.1_ASM221679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:15,148] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:15,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:15,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:15,164] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:15,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:15,165] [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
Brachybacterium avium	strain=VR2415	GCA_002216795.1	2017485	2017485	type	True	100.0	1188	1188	95	conclusive
Brachybacterium vulturis	strain=VM2412	GCA_002407185.1	2017484	2017484	type	True	90.5675	995	1188	95	below_threshold
Brachybacterium faecium	strain=DSM 4810	GCA_000023405.1	43669	43669	type	True	85.4887	869	1188	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	85.4172	884	1188	95	below_threshold
Brachybacterium massiliense	strain=mt5	GCA_900184245.1	1755098	1755098	type	True	84.6564	868	1188	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	84.2984	842	1188	95	below_threshold
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	83.4165	759	1188	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	81.2432	593	1188	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	80.1838	580	1188	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	80.1482	590	1188	95	below_threshold
Occultella aeris	strain=CIP 111667	GCA_902703175.1	2761496	2761496	type	True	76.7772	261	1188	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.758	255	1188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:15,166] [INFO] DFAST Taxonomy check result was written to GCF_002216795.1_ASM221679v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:15,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:15,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:15,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference/checkm_data
[2024-01-24 14:56:15,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:15,208] [INFO] Task started: CheckM
[2024-01-24 14:56:15,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002216795.1_ASM221679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002216795.1_ASM221679v1_genomic.fna/checkm_input GCF_002216795.1_ASM221679v1_genomic.fna/checkm_result
[2024-01-24 14:57:20,508] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:20,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:20,534] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:20,534] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:20,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002216795.1_ASM221679v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:20,535] [INFO] Task started: Blastn
[2024-01-24 14:57:20,536] [INFO] Running command: blastn -query GCF_002216795.1_ASM221679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4fc1fac-9cf0-4c9b-801b-75a4e86c3e43/dqc_reference/reference_markers_gtdb.fasta -out GCF_002216795.1_ASM221679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:22,456] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:22,460] [INFO] Selected 9 target genomes.
[2024-01-24 14:57:22,460] [INFO] Target genome list was writen to GCF_002216795.1_ASM221679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:22,484] [INFO] Task started: fastANI
[2024-01-24 14:57:22,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf4d720c-58a3-489e-b2a5-cdb8fe1801d6/GCF_002216795.1_ASM221679v1_genomic.fna.gz --refList GCF_002216795.1_ASM221679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002216795.1_ASM221679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:30,603] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:30,614] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:30,614] [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_002216795.1	s__Brachybacterium avium	100.0	1188	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002407185.1	s__Brachybacterium vulturis	90.575	996	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023405.1	s__Brachybacterium faecium	85.503	870	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407065.1	s__Brachybacterium ginsengisoli	85.4313	883	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184245.1	s__Brachybacterium massiliense	84.6486	871	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014400405.1	s__Brachybacterium sp014400405	84.4253	857	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355475.1	s__Brachybacterium saurashtrense	84.4061	835	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCA_012799425.1	s__Brachybacterium sp012799425	83.5835	559	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118275.1	s__Brachybacterium merdavium	81.1103	684	1188	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:30,615] [INFO] GTDB search result was written to GCF_002216795.1_ASM221679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:30,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:30,619] [INFO] DFAST_QC result json was written to GCF_002216795.1_ASM221679v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:30,619] [INFO] DFAST_QC completed!
[2024-01-24 14:57:30,619] [INFO] Total running time: 0h1m40s