[2024-01-24 11:34:40,521] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:40,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:40,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference
[2024-01-24 11:34:41,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,874] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,874] [INFO] Running command: gunzip -c /var/lib/cwl/stg496094b7-c4cb-4ffa-8f91-3a68fc13a97a/GCF_011617705.1_ASM1161770v1_genomic.fna.gz | prodigal -d GCF_011617705.1_ASM1161770v1_genomic.fna/cds.fna -a GCF_011617705.1_ASM1161770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:54,381] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:54,382] [INFO] Task started: HMMsearch
[2024-01-24 11:34:54,382] [INFO] Running command: hmmsearch --tblout GCF_011617705.1_ASM1161770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference/reference_markers.hmm GCF_011617705.1_ASM1161770v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,675] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,726] [INFO] Query marker FASTA was written to GCF_011617705.1_ASM1161770v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,727] [INFO] Task started: Blastn
[2024-01-24 11:34:54,727] [INFO] Running command: blastn -query GCF_011617705.1_ASM1161770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference/reference_markers.fasta -out GCF_011617705.1_ASM1161770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,822] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,826] [INFO] Selected 15 target genomes.
[2024-01-24 11:34:55,826] [INFO] Target genome list was writen to GCF_011617705.1_ASM1161770v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,853] [INFO] Task started: fastANI
[2024-01-24 11:34:55,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg496094b7-c4cb-4ffa-8f91-3a68fc13a97a/GCF_011617705.1_ASM1161770v1_genomic.fna.gz --refList GCF_011617705.1_ASM1161770v1_genomic.fna/target_genomes.txt --output GCF_011617705.1_ASM1161770v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:09,414] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:09,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:09,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:09,428] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:09,428] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:09,428] [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 limosum	strain=o2	GCA_011617705.1	2697565	2697565	type	True	100.0	1417	1417	95	conclusive
Brevibacterium pigmentatum	strain=YB235	GCA_011617465.1	1496080	1496080	type	True	89.9656	1143	1417	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	89.9611	1101	1417	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	89.9122	1104	1417	95	below_threshold
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	89.7573	1037	1417	95	below_threshold
Brevibacterium epidermidis	strain=NBRC 14811	GCA_001570805.1	1698	1698	type	True	89.6907	1074	1417	95	below_threshold
Brevibacterium iodinum	strain=ATCC 49514	GCA_900169265.1	31943	31943	type	True	89.5779	996	1417	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_900169165.1	1703	1703	suspected-type	True	89.5647	1050	1417	95	below_threshold
Brevibacterium linens	strain=ATCC 9172	GCA_008868375.1	1703	1703	suspected-type	True	89.537	1045	1417	95	below_threshold
Brevibacterium siliguriense	strain=DSM 23676	GCA_900105315.1	1136497	1136497	type	True	89.3359	1107	1417	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	81.1863	871	1417	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	80.9861	842	1417	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	78.6475	405	1417	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	77.9956	328	1417	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	76.64	184	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:09,444] [INFO] DFAST Taxonomy check result was written to GCF_011617705.1_ASM1161770v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:09,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:09,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:09,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference/checkm_data
[2024-01-24 11:35:09,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:09,512] [INFO] Task started: CheckM
[2024-01-24 11:35:09,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011617705.1_ASM1161770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011617705.1_ASM1161770v1_genomic.fna/checkm_input GCF_011617705.1_ASM1161770v1_genomic.fna/checkm_result
[2024-01-24 11:36:15,999] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:16,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,017] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:16,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:16,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011617705.1_ASM1161770v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:16,017] [INFO] Task started: Blastn
[2024-01-24 11:36:16,017] [INFO] Running command: blastn -query GCF_011617705.1_ASM1161770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8eff1f-f3cf-45e6-8a18-7f860f2e23b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_011617705.1_ASM1161770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:17,534] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:17,537] [INFO] Selected 10 target genomes.
[2024-01-24 11:36:17,537] [INFO] Target genome list was writen to GCF_011617705.1_ASM1161770v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:17,544] [INFO] Task started: fastANI
[2024-01-24 11:36:17,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg496094b7-c4cb-4ffa-8f91-3a68fc13a97a/GCF_011617705.1_ASM1161770v1_genomic.fna.gz --refList GCF_011617705.1_ASM1161770v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011617705.1_ASM1161770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:28,193] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:28,202] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:28,202] [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_011617705.1	s__Brevibacterium sp011617705	100.0	1417	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.55	96.55	0.87	0.87	2	conclusive
GCF_004745485.1	s__Brevibacterium sp004745485	89.9782	1097	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011617465.1	s__Brevibacterium sp011617465	89.9723	1144	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623905.1	s__Brevibacterium sediminis	89.9611	1101	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCF_012844365.1	s__Brevibacterium sp012844365	89.8981	1159	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013280495.1	s__Brevibacterium permense	89.7384	1039	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570805.1	s__Brevibacterium epidermidis	89.6961	1073	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.16	95.79	0.90	0.89	4	-
GCF_900169165.1	s__Brevibacterium linens	89.5791	1049	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.12	96.02	0.90	0.82	5	-
GCF_900169265.1	s__Brevibacterium iodinum	89.5779	996	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105315.1	s__Brevibacterium siliguriense	89.3283	1105	1417	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 11:36:28,204] [INFO] GTDB search result was written to GCF_011617705.1_ASM1161770v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:28,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:28,208] [INFO] DFAST_QC result json was written to GCF_011617705.1_ASM1161770v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:28,208] [INFO] DFAST_QC completed!
[2024-01-24 11:36:28,208] [INFO] Total running time: 0h1m48s