[2024-01-24 12:22:27,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:27,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:27,286] [INFO] DQC Reference Directory: /var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference
[2024-01-24 12:22:28,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:28,661] [INFO] Task started: Prodigal
[2024-01-24 12:22:28,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg4588143d-fe19-4c74-bba7-472d68b7daa7/GCF_000982825.1_ASM98282v1_genomic.fna.gz | prodigal -d GCF_000982825.1_ASM98282v1_genomic.fna/cds.fna -a GCF_000982825.1_ASM98282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:41,858] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:41,859] [INFO] Task started: HMMsearch
[2024-01-24 12:22:41,859] [INFO] Running command: hmmsearch --tblout GCF_000982825.1_ASM98282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference/reference_markers.hmm GCF_000982825.1_ASM98282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:42,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:42,211] [INFO] Found 6/6 markers.
[2024-01-24 12:22:42,251] [INFO] Query marker FASTA was written to GCF_000982825.1_ASM98282v1_genomic.fna/markers.fasta
[2024-01-24 12:22:42,251] [INFO] Task started: Blastn
[2024-01-24 12:22:42,251] [INFO] Running command: blastn -query GCF_000982825.1_ASM98282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference/reference_markers.fasta -out GCF_000982825.1_ASM98282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:43,262] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:43,266] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:43,267] [INFO] Target genome list was writen to GCF_000982825.1_ASM98282v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:43,269] [INFO] Task started: fastANI
[2024-01-24 12:22:43,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg4588143d-fe19-4c74-bba7-472d68b7daa7/GCF_000982825.1_ASM98282v1_genomic.fna.gz --refList GCF_000982825.1_ASM98282v1_genomic.fna/target_genomes.txt --output GCF_000982825.1_ASM98282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:57,022] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:57,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:57,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:57,032] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:22:57,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:57,032] [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 sakazakii	strain=ATCC 29544	GCA_000982825.1	28141	28141	type	True	100.0	1547	1552	95	conclusive
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	99.9943	1537	1552	95	conclusive
Cronobacter sakazakii	strain=NBRC 102416	GCA_000684935.1	28141	28141	type	True	99.9715	1453	1552	95	conclusive
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	99.8073	1314	1552	95	conclusive
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	94.963	1355	1552	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	94.8951	1301	1552	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.5635	829	1552	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.4004	857	1552	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.0312	833	1552	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.8004	825	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:57,035] [INFO] DFAST Taxonomy check result was written to GCF_000982825.1_ASM98282v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:57,036] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:57,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:57,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference/checkm_data
[2024-01-24 12:22:57,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:57,090] [INFO] Task started: CheckM
[2024-01-24 12:22:57,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000982825.1_ASM98282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000982825.1_ASM98282v1_genomic.fna/checkm_input GCF_000982825.1_ASM98282v1_genomic.fna/checkm_result
[2024-01-24 12:23:37,314] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:37,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:37,342] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:37,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:37,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000982825.1_ASM98282v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:37,343] [INFO] Task started: Blastn
[2024-01-24 12:23:37,343] [INFO] Running command: blastn -query GCF_000982825.1_ASM98282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga988c690-12e0-47a9-a434-d1c96467fcaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000982825.1_ASM98282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:38,563] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:38,568] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:38,568] [INFO] Target genome list was writen to GCF_000982825.1_ASM98282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:38,587] [INFO] Task started: fastANI
[2024-01-24 12:23:38,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg4588143d-fe19-4c74-bba7-472d68b7daa7/GCF_000982825.1_ASM98282v1_genomic.fna.gz --refList GCF_000982825.1_ASM98282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000982825.1_ASM98282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:50,347] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:50,355] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:50,356] [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_000982825.1	s__Cronobacter sakazakii	100.0	1546	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	conclusive
GCF_001277215.2	s__Cronobacter malonaticus	94.963	1355	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_001277175.1	s__Cronobacter universalis	93.6843	1324	1552	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	92.3675	1339	1552	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	89.6018	1278	1552	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	89.5387	1257	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_006171285.1	s__Leclercia adecarboxylata_A	81.5659	856	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	97.80	96.55	0.92	0.89	4	-
GCF_001266615.1	s__Kluyvera cryocrescens_A	79.9983	682	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590905.1	s__Serratia grimesii	78.3071	384	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.09	98.89	0.96	0.93	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:50,357] [INFO] GTDB search result was written to GCF_000982825.1_ASM98282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:50,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:50,363] [INFO] DFAST_QC result json was written to GCF_000982825.1_ASM98282v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:50,363] [INFO] DFAST_QC completed!
[2024-01-24 12:23:50,363] [INFO] Total running time: 0h1m23s