[2024-01-24 12:31:04,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference
[2024-01-24 12:31:05,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,841] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3143c98-9de1-425a-b448-b2c24746e78e/GCF_016107685.1_ASM1610768v1_genomic.fna.gz | prodigal -d GCF_016107685.1_ASM1610768v1_genomic.fna/cds.fna -a GCF_016107685.1_ASM1610768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:16,912] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:16,913] [INFO] Task started: HMMsearch
[2024-01-24 12:31:16,913] [INFO] Running command: hmmsearch --tblout GCF_016107685.1_ASM1610768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference/reference_markers.hmm GCF_016107685.1_ASM1610768v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:17,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:17,212] [INFO] Found 6/6 markers.
[2024-01-24 12:31:17,253] [INFO] Query marker FASTA was written to GCF_016107685.1_ASM1610768v1_genomic.fna/markers.fasta
[2024-01-24 12:31:17,253] [INFO] Task started: Blastn
[2024-01-24 12:31:17,254] [INFO] Running command: blastn -query GCF_016107685.1_ASM1610768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference/reference_markers.fasta -out GCF_016107685.1_ASM1610768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:18,269] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:18,273] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:18,273] [INFO] Target genome list was writen to GCF_016107685.1_ASM1610768v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:18,280] [INFO] Task started: fastANI
[2024-01-24 12:31:18,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3143c98-9de1-425a-b448-b2c24746e78e/GCF_016107685.1_ASM1610768v1_genomic.fna.gz --refList GCF_016107685.1_ASM1610768v1_genomic.fna/target_genomes.txt --output GCF_016107685.1_ASM1610768v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:27,838] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:27,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:27,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:27,855] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:27,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:27,855] [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 yomogidense	strain=DSM 24850	GCA_016107685.1	946573	946573	type	True	100.0	1228	1228	95	conclusive
Brevibacterium senegalense	strain=JC43	GCA_000285835.2	1033736	1033736	type	True	82.5263	756	1228	95	below_threshold
Brevibacterium jeotgali	strain=SJ5-8	GCA_900169175.1	1262550	1262550	type	True	82.1333	776	1228	95	below_threshold
Brevibacterium jeotgali	strain=DSM 29217	GCA_007828155.1	1262550	1262550	type	True	82.0763	766	1228	95	below_threshold
Brevibacterium album	strain=DSM 18261	GCA_000426445.1	417948	417948	type	True	79.2179	595	1228	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	78.7416	360	1228	95	below_threshold
Brevibacterium ihuae	strain=CV3	GCA_900184225.1	1631743	1631743	type	True	78.7031	407	1228	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	77.7397	366	1228	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	77.1826	237	1228	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	76.939	218	1228	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	76.4317	125	1228	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	76.3839	158	1228	95	below_threshold
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	75.721	189	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:27,857] [INFO] DFAST Taxonomy check result was written to GCF_016107685.1_ASM1610768v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:27,857] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:27,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:27,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference/checkm_data
[2024-01-24 12:31:27,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:27,894] [INFO] Task started: CheckM
[2024-01-24 12:31:27,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016107685.1_ASM1610768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016107685.1_ASM1610768v1_genomic.fna/checkm_input GCF_016107685.1_ASM1610768v1_genomic.fna/checkm_result
[2024-01-24 12:32:28,409] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:28,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:28,431] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:28,432] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:28,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016107685.1_ASM1610768v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:28,433] [INFO] Task started: Blastn
[2024-01-24 12:32:28,433] [INFO] Running command: blastn -query GCF_016107685.1_ASM1610768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca66aa3a-050c-42e5-bfbb-7824a4c4ad78/dqc_reference/reference_markers_gtdb.fasta -out GCF_016107685.1_ASM1610768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:29,960] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:29,965] [INFO] Selected 6 target genomes.
[2024-01-24 12:32:29,965] [INFO] Target genome list was writen to GCF_016107685.1_ASM1610768v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:29,971] [INFO] Task started: fastANI
[2024-01-24 12:32:29,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3143c98-9de1-425a-b448-b2c24746e78e/GCF_016107685.1_ASM1610768v1_genomic.fna.gz --refList GCF_016107685.1_ASM1610768v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016107685.1_ASM1610768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:34,882] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:34,892] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:34,892] [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_016107685.1	s__Brevibacterium yomogidense	100.0	1228	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900163715.1	s__Brevibacterium yomogidense_A	82.6249	782	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.08	97.08	0.87	0.87	2	-
GCF_000285835.1	s__Brevibacterium senegalense	82.5369	755	1228	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	82.1828	536	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169175.1	s__Brevibacterium jeotgali	82.1333	776	1228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000426445.1	s__Brevibacterium album	79.1905	599	1228	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 12:32:34,894] [INFO] GTDB search result was written to GCF_016107685.1_ASM1610768v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:34,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:34,898] [INFO] DFAST_QC result json was written to GCF_016107685.1_ASM1610768v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:34,898] [INFO] DFAST_QC completed!
[2024-01-24 12:32:34,898] [INFO] Total running time: 0h1m30s