[2024-01-24 12:22:48,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference
[2024-01-24 12:22:49,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,214] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4fa6524-5fa4-4c4c-a650-7882cd05d535/GCF_005484965.1_ASM548496v1_genomic.fna.gz | prodigal -d GCF_005484965.1_ASM548496v1_genomic.fna/cds.fna -a GCF_005484965.1_ASM548496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:00,782] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:00,783] [INFO] Task started: HMMsearch
[2024-01-24 12:23:00,783] [INFO] Running command: hmmsearch --tblout GCF_005484965.1_ASM548496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference/reference_markers.hmm GCF_005484965.1_ASM548496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:01,090] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:01,091] [INFO] Found 6/6 markers.
[2024-01-24 12:23:01,127] [INFO] Query marker FASTA was written to GCF_005484965.1_ASM548496v1_genomic.fna/markers.fasta
[2024-01-24 12:23:01,127] [INFO] Task started: Blastn
[2024-01-24 12:23:01,127] [INFO] Running command: blastn -query GCF_005484965.1_ASM548496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference/reference_markers.fasta -out GCF_005484965.1_ASM548496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:02,875] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:02,877] [INFO] Selected 18 target genomes.
[2024-01-24 12:23:02,877] [INFO] Target genome list was writen to GCF_005484965.1_ASM548496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:02,945] [INFO] Task started: fastANI
[2024-01-24 12:23:02,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4fa6524-5fa4-4c4c-a650-7882cd05d535/GCF_005484965.1_ASM548496v1_genomic.fna.gz --refList GCF_005484965.1_ASM548496v1_genomic.fna/target_genomes.txt --output GCF_005484965.1_ASM548496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:20,705] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:20,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:20,715] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:20,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:20,715] [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
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	100.0	1629	1630	95	conclusive
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	99.961	1565	1630	95	conclusive
Brenneria alni	strain=NCPPB 3934	GCA_003666245.1	71656	71656	type	True	84.5953	965	1630	95	below_threshold
Brenneria izadpanahii	strain=Iran 50	GCA_017569925.1	2722756	2722756	type	True	84.1388	1047	1630	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_002291445.1	1109412	1109412	type	True	83.9725	1064	1630	95	below_threshold
Brenneria goodwinii	strain=FRB141	GCA_003666235.1	1109412	1109412	type	True	83.8559	1036	1630	95	below_threshold
Brenneria roseae subsp. americana	strain=LMG 27715	GCA_003115815.1	1508507	1509241	type	True	81.9278	933	1630	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	81.8521	907	1630	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	80.6471	747	1630	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.5213	579	1630	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.3773	558	1630	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.2484	555	1630	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	79.0347	528	1630	95	below_threshold
Citrobacter youngae	strain=NCTC13709	GCA_900638065.1	133448	133448	type	True	78.5665	293	1630	95	below_threshold
Citrobacter youngae	strain=CCUG 30791	GCA_003818115.1	133448	133448	type	True	77.9586	286	1630	95	below_threshold
Citrobacter braakii	strain=ATCC 51113	GCA_002075345.1	57706	57706	type	True	77.9346	287	1630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,717] [INFO] DFAST Taxonomy check result was written to GCF_005484965.1_ASM548496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:20,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:20,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:20,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference/checkm_data
[2024-01-24 12:23:20,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:20,765] [INFO] Task started: CheckM
[2024-01-24 12:23:20,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005484965.1_ASM548496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005484965.1_ASM548496v1_genomic.fna/checkm_input GCF_005484965.1_ASM548496v1_genomic.fna/checkm_result
[2024-01-24 12:23:55,555] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:55,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:55,574] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:55,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:55,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005484965.1_ASM548496v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:55,574] [INFO] Task started: Blastn
[2024-01-24 12:23:55,574] [INFO] Running command: blastn -query GCF_005484965.1_ASM548496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fe89b74-630e-4714-bfb0-60c7abdb1e60/dqc_reference/reference_markers_gtdb.fasta -out GCF_005484965.1_ASM548496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:56,632] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:56,635] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:56,635] [INFO] Target genome list was writen to GCF_005484965.1_ASM548496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:56,641] [INFO] Task started: fastANI
[2024-01-24 12:23:56,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4fa6524-5fa4-4c4c-a650-7882cd05d535/GCF_005484965.1_ASM548496v1_genomic.fna.gz --refList GCF_005484965.1_ASM548496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005484965.1_ASM548496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:07,780] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:07,787] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:07,787] [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_005484965.1	s__Brenneria nigrifluens	100.0	1629	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	conclusive
GCF_013155275.1	s__Brenneria sp013155275	85.1138	1017	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.39	99.39	0.93	0.93	2	-
GCF_003666245.1	s__Brenneria alni	84.5828	966	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569925.1	s__Brenneria izadpanahii	84.1202	1048	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002291445.1	s__Brenneria goodwinii	83.9759	1065	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	99.30	98.94	0.94	0.91	4	-
GCF_005484945.1	s__Brenneria rubrifaciens	81.9961	826	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003115845.1	s__Brenneria roseae	81.8488	909	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	96.57	96.57	0.91	0.91	2	-
GCF_015999465.1	s__Lonsdalea populi	79.7734	541	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.60	99.19	0.97	0.95	28	-
GCF_001976145.1	s__Chania oryzae	78.5124	433	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_900094795.1	s__Kosakonia oryziphila	77.8116	365	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:07,788] [INFO] GTDB search result was written to GCF_005484965.1_ASM548496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:07,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:07,792] [INFO] DFAST_QC result json was written to GCF_005484965.1_ASM548496v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:07,792] [INFO] DFAST_QC completed!
[2024-01-24 12:24:07,792] [INFO] Total running time: 0h1m20s