[2024-01-24 13:49:40,023] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,025] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,025] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference
[2024-01-24 13:49:41,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,132] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,132] [INFO] Running command: gunzip -c /var/lib/cwl/stgc505260a-6d09-4091-9d4d-2f554640b56e/GCF_016027855.1_ASM1602785v1_genomic.fna.gz | prodigal -d GCF_016027855.1_ASM1602785v1_genomic.fna/cds.fna -a GCF_016027855.1_ASM1602785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:52,081] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:52,081] [INFO] Task started: HMMsearch
[2024-01-24 13:49:52,081] [INFO] Running command: hmmsearch --tblout GCF_016027855.1_ASM1602785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference/reference_markers.hmm GCF_016027855.1_ASM1602785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:52,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:52,311] [INFO] Found 6/6 markers.
[2024-01-24 13:49:52,345] [INFO] Query marker FASTA was written to GCF_016027855.1_ASM1602785v1_genomic.fna/markers.fasta
[2024-01-24 13:49:52,345] [INFO] Task started: Blastn
[2024-01-24 13:49:52,345] [INFO] Running command: blastn -query GCF_016027855.1_ASM1602785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference/reference_markers.fasta -out GCF_016027855.1_ASM1602785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:53,199] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:53,201] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:53,201] [INFO] Target genome list was writen to GCF_016027855.1_ASM1602785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:53,209] [INFO] Task started: fastANI
[2024-01-24 13:49:53,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgc505260a-6d09-4091-9d4d-2f554640b56e/GCF_016027855.1_ASM1602785v1_genomic.fna.gz --refList GCF_016027855.1_ASM1602785v1_genomic.fna/target_genomes.txt --output GCF_016027855.1_ASM1602785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:12,563] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:12,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:12,577] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:50:12,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:12,577] [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
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	100.0	1516	1518	95	conclusive
Atlantibacter hermannii	strain=NBRC 105704	GCA_000248015.2	565	565	type	True	99.9816	1473	1518	95	conclusive
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	81.155	794	1518	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_000982825.1	28141	28141	type	True	81.1344	802	1518	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	81.0901	787	1518	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	80.9622	810	1518	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	80.9435	762	1518	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	80.8826	760	1518	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	80.8745	779	1518	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	80.8607	738	1518	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	80.6679	742	1518	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	80.5434	698	1518	95	below_threshold
Siccibacter colletis	strain=1383	GCA_000696575.1	1505757	1505757	type	True	80.5356	715	1518	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.4967	771	1518	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.4049	718	1518	95	below_threshold
Citrobacter freundii	strain=ATCC 8090	GCA_011064845.1	546	546	type	True	80.344	672	1518	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.3375	710	1518	95	below_threshold
Klebsiella aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	80.3292	703	1518	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	80.2402	743	1518	95	below_threshold
Citrobacter freundii	strain=MTCC 1658	GCA_000312465.1	546	546	type	True	80.1067	661	1518	95	below_threshold
Citrobacter freundii	strain=NBRC 12681	GCA_000759735.1	546	546	type	True	80.0511	661	1518	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	79.977	683	1518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,578] [INFO] DFAST Taxonomy check result was written to GCF_016027855.1_ASM1602785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:12,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:12,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:12,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference/checkm_data
[2024-01-24 13:50:12,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:12,620] [INFO] Task started: CheckM
[2024-01-24 13:50:12,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027855.1_ASM1602785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027855.1_ASM1602785v1_genomic.fna/checkm_input GCF_016027855.1_ASM1602785v1_genomic.fna/checkm_result
[2024-01-24 13:50:46,269] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:46,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:46,284] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:46,284] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:46,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027855.1_ASM1602785v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:46,284] [INFO] Task started: Blastn
[2024-01-24 13:50:46,284] [INFO] Running command: blastn -query GCF_016027855.1_ASM1602785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3240d19-0092-46ba-91f2-cb3a66aa96ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027855.1_ASM1602785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:47,679] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:47,681] [INFO] Selected 5 target genomes.
[2024-01-24 13:50:47,681] [INFO] Target genome list was writen to GCF_016027855.1_ASM1602785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:47,684] [INFO] Task started: fastANI
[2024-01-24 13:50:47,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgc505260a-6d09-4091-9d4d-2f554640b56e/GCF_016027855.1_ASM1602785v1_genomic.fna.gz --refList GCF_016027855.1_ASM1602785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027855.1_ASM1602785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:53,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:53,715] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:53,715] [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
GCA_900635495.1	s__Atlantibacter hermannii	99.9569	1514	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	conclusive
GCF_007570865.1	s__Atlantibacter subterranea	86.4386	1171	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
GCF_009907385.1	s__Atlantibacter hermannii_A	86.3032	1169	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193285.1	s__Atlantibacter sp002345315	86.2812	1200	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_011077955.1	s__Atlantibacter sp002358165	86.2749	1179	1518	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	99.01	98.64	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:53,718] [INFO] GTDB search result was written to GCF_016027855.1_ASM1602785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:53,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:53,722] [INFO] DFAST_QC result json was written to GCF_016027855.1_ASM1602785v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:53,722] [INFO] DFAST_QC completed!
[2024-01-24 13:50:53,722] [INFO] Total running time: 0h1m14s