[2024-01-24 10:47:54,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stge0a863a4-fb91-4b95-82d2-1f0461adbfbb/GCF_007828155.1_ASM782815v1_genomic.fna.gz | prodigal -d GCF_007828155.1_ASM782815v1_genomic.fna/cds.fna -a GCF_007828155.1_ASM782815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:13,197] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:13,197] [INFO] Task started: HMMsearch
[2024-01-24 10:48:13,197] [INFO] Running command: hmmsearch --tblout GCF_007828155.1_ASM782815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference/reference_markers.hmm GCF_007828155.1_ASM782815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:13,468] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:13,470] [INFO] Found 6/6 markers.
[2024-01-24 10:48:13,500] [INFO] Query marker FASTA was written to GCF_007828155.1_ASM782815v1_genomic.fna/markers.fasta
[2024-01-24 10:48:13,501] [INFO] Task started: Blastn
[2024-01-24 10:48:13,501] [INFO] Running command: blastn -query GCF_007828155.1_ASM782815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference/reference_markers.fasta -out GCF_007828155.1_ASM782815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:14,490] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:14,494] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:14,495] [INFO] Target genome list was writen to GCF_007828155.1_ASM782815v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:15,613] [INFO] Task started: fastANI
[2024-01-24 10:48:15,614] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a863a4-fb91-4b95-82d2-1f0461adbfbb/GCF_007828155.1_ASM782815v1_genomic.fna.gz --refList GCF_007828155.1_ASM782815v1_genomic.fna/target_genomes.txt --output GCF_007828155.1_ASM782815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:23,965] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:23,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:23,966] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:23,976] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:23,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:23,976] [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
Brevibacterium jeotgali	strain=DSM 29217	GCA_007828155.1	1262550	1262550	type	True	100.0	1107	1109	95	conclusive
Brevibacterium jeotgali	strain=SJ5-8	GCA_900169175.1	1262550	1262550	type	True	99.9629	1062	1109	95	conclusive
Brevibacterium yomogidense	strain=DSM 24850	GCA_016107685.1	946573	946573	type	True	82.167	773	1109	95	below_threshold
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	81.5308	674	1109	95	below_threshold
Brevibacterium album	strain=DSM 18261	GCA_000426445.1	417948	417948	type	True	79.3245	510	1109	95	below_threshold
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	78.9506	386	1109	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	78.3967	332	1109	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	77.8431	306	1109	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	77.2903	132	1109	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.6398	149	1109	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4971	174	1109	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:23,979] [INFO] DFAST Taxonomy check result was written to GCF_007828155.1_ASM782815v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:23,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:23,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:23,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference/checkm_data
[2024-01-24 10:48:23,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:24,016] [INFO] Task started: CheckM
[2024-01-24 10:48:24,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007828155.1_ASM782815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007828155.1_ASM782815v1_genomic.fna/checkm_input GCF_007828155.1_ASM782815v1_genomic.fna/checkm_result
[2024-01-24 10:49:21,991] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:21,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:22,013] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:22,013] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:22,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007828155.1_ASM782815v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:22,014] [INFO] Task started: Blastn
[2024-01-24 10:49:22,014] [INFO] Running command: blastn -query GCF_007828155.1_ASM782815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef1d0e44-c2bf-4218-9549-75f022745e76/dqc_reference/reference_markers_gtdb.fasta -out GCF_007828155.1_ASM782815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:23,469] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:23,473] [INFO] Selected 8 target genomes.
[2024-01-24 10:49:23,473] [INFO] Target genome list was writen to GCF_007828155.1_ASM782815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:23,497] [INFO] Task started: fastANI
[2024-01-24 10:49:23,497] [INFO] Running command: fastANI --query /var/lib/cwl/stge0a863a4-fb91-4b95-82d2-1f0461adbfbb/GCF_007828155.1_ASM782815v1_genomic.fna.gz --refList GCF_007828155.1_ASM782815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007828155.1_ASM782815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:29,520] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:29,533] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:29,534] [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_900169175.1	s__Brevibacterium jeotgali	99.9629	1062	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_900163715.1	s__Brevibacterium yomogidense_A	89.5545	891	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.08	97.08	0.87	0.87	2	-
GCF_016107685.1	s__Brevibacterium yomogidense	82.1266	778	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285835.1	s__Brevibacterium senegalense	81.5312	674	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019117325.1	s__Brevibacterium intestinigallinarum	80.9181	507	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426445.1	s__Brevibacterium album	79.3154	511	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184225.1	s__Brevibacterium ihuae	78.9431	383	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280295.1	s__Brevibacterium sp005280295	78.7537	395	1109	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:29,535] [INFO] GTDB search result was written to GCF_007828155.1_ASM782815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:29,536] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:29,539] [INFO] DFAST_QC result json was written to GCF_007828155.1_ASM782815v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:29,539] [INFO] DFAST_QC completed!
[2024-01-24 10:49:29,539] [INFO] Total running time: 0h1m35s