[2024-01-24 13:10:19,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference
[2024-01-24 13:10:20,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,745] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg00b53b35-ad5f-4441-aa7b-b5298d9455d6/GCF_000409305.1_Cmal825_final_contigs_genomic.fna.gz | prodigal -d GCF_000409305.1_Cmal825_final_contigs_genomic.fna/cds.fna -a GCF_000409305.1_Cmal825_final_contigs_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:32,255] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:32,255] [INFO] Task started: HMMsearch
[2024-01-24 13:10:32,255] [INFO] Running command: hmmsearch --tblout GCF_000409305.1_Cmal825_final_contigs_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference/reference_markers.hmm GCF_000409305.1_Cmal825_final_contigs_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:32,607] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:32,608] [INFO] Found 6/6 markers.
[2024-01-24 13:10:32,649] [INFO] Query marker FASTA was written to GCF_000409305.1_Cmal825_final_contigs_genomic.fna/markers.fasta
[2024-01-24 13:10:32,649] [INFO] Task started: Blastn
[2024-01-24 13:10:32,650] [INFO] Running command: blastn -query GCF_000409305.1_Cmal825_final_contigs_genomic.fna/markers.fasta -db /var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference/reference_markers.fasta -out GCF_000409305.1_Cmal825_final_contigs_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:33,644] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:33,649] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:33,650] [INFO] Target genome list was writen to GCF_000409305.1_Cmal825_final_contigs_genomic.fna/target_genomes.txt
[2024-01-24 13:10:33,656] [INFO] Task started: fastANI
[2024-01-24 13:10:33,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b53b35-ad5f-4441-aa7b-b5298d9455d6/GCF_000409305.1_Cmal825_final_contigs_genomic.fna.gz --refList GCF_000409305.1_Cmal825_final_contigs_genomic.fna/target_genomes.txt --output GCF_000409305.1_Cmal825_final_contigs_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:47,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:47,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:47,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:47,195] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:47,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:47,195] [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
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	100.0	1416	1419	95	conclusive
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	99.9919	1415	1419	95	conclusive
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	94.8861	1305	1419	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	94.857	1200	1419	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_000982825.1	28141	28141	type	True	94.8527	1307	1419	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_001277175.1	535744	535744	type	True	94.2526	1283	1419	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	94.2483	1262	1419	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	94.2359	1286	1419	95	below_threshold
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	93.9707	1276	1419	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.2755	833	1419	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.2313	840	1419	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.1297	809	1419	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.031	769	1419	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:47,198] [INFO] DFAST Taxonomy check result was written to GCF_000409305.1_Cmal825_final_contigs_genomic.fna/tc_result.tsv
[2024-01-24 13:10:47,199] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:47,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:47,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference/checkm_data
[2024-01-24 13:10:47,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:47,254] [INFO] Task started: CheckM
[2024-01-24 13:10:47,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000409305.1_Cmal825_final_contigs_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000409305.1_Cmal825_final_contigs_genomic.fna/checkm_input GCF_000409305.1_Cmal825_final_contigs_genomic.fna/checkm_result
[2024-01-24 13:11:25,016] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:25,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:25,038] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:25,038] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:25,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000409305.1_Cmal825_final_contigs_genomic.fna/markers.fasta)
[2024-01-24 13:11:25,039] [INFO] Task started: Blastn
[2024-01-24 13:11:25,039] [INFO] Running command: blastn -query GCF_000409305.1_Cmal825_final_contigs_genomic.fna/markers.fasta -db /var/lib/cwl/stg00fdc374-946d-41ef-a5ba-5bb985d11195/dqc_reference/reference_markers_gtdb.fasta -out GCF_000409305.1_Cmal825_final_contigs_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:26,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:26,637] [INFO] Selected 6 target genomes.
[2024-01-24 13:11:26,637] [INFO] Target genome list was writen to GCF_000409305.1_Cmal825_final_contigs_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:26,644] [INFO] Task started: fastANI
[2024-01-24 13:11:26,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b53b35-ad5f-4441-aa7b-b5298d9455d6/GCF_000409305.1_Cmal825_final_contigs_genomic.fna.gz --refList GCF_000409305.1_Cmal825_final_contigs_genomic.fna/target_genomes_gtdb.txt --output GCF_000409305.1_Cmal825_final_contigs_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:34,557] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:34,568] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:34,569] [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_001277215.2	s__Cronobacter malonaticus	99.9919	1415	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	conclusive
GCF_000982825.1	s__Cronobacter sakazakii	94.8417	1308	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCF_001277175.1	s__Cronobacter universalis	94.2526	1283	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCA_000027065.2	s__Cronobacter turicensis	92.6167	1300	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277235.1	s__Cronobacter dublinensis	89.6303	1245	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_001277195.1	s__Cronobacter muytjensii	89.5645	1233	1419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:34,570] [INFO] GTDB search result was written to GCF_000409305.1_Cmal825_final_contigs_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:34,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:34,574] [INFO] DFAST_QC result json was written to GCF_000409305.1_Cmal825_final_contigs_genomic.fna/dqc_result.json
[2024-01-24 13:11:34,574] [INFO] DFAST_QC completed!
[2024-01-24 13:11:34,575] [INFO] Total running time: 0h1m15s