[2023-06-19 13:54:35,147] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:35,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:35,152] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference
[2023-06-19 13:54:36,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:36,422] [INFO] Task started: Prodigal
[2023-06-19 13:54:36,423] [INFO] Running command: gunzip -c /var/lib/cwl/stgab5cda5d-954d-469f-a93b-1bca4abbce97/GCA_014858255.1_ASM1485825v1_genomic.fna.gz | prodigal -d GCA_014858255.1_ASM1485825v1_genomic.fna/cds.fna -a GCA_014858255.1_ASM1485825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:41,049] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:41,049] [INFO] Task started: HMMsearch
[2023-06-19 13:54:41,049] [INFO] Running command: hmmsearch --tblout GCA_014858255.1_ASM1485825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference/reference_markers.hmm GCA_014858255.1_ASM1485825v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:41,281] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:41,282] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab5cda5d-954d-469f-a93b-1bca4abbce97/GCA_014858255.1_ASM1485825v1_genomic.fna.gz]
[2023-06-19 13:54:41,311] [INFO] Query marker FASTA was written to GCA_014858255.1_ASM1485825v1_genomic.fna/markers.fasta
[2023-06-19 13:54:41,312] [INFO] Task started: Blastn
[2023-06-19 13:54:41,312] [INFO] Running command: blastn -query GCA_014858255.1_ASM1485825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference/reference_markers.fasta -out GCA_014858255.1_ASM1485825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:42,154] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:42,158] [INFO] Selected 10 target genomes.
[2023-06-19 13:54:42,159] [INFO] Target genome list was writen to GCA_014858255.1_ASM1485825v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:42,161] [INFO] Task started: fastANI
[2023-06-19 13:54:42,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgab5cda5d-954d-469f-a93b-1bca4abbce97/GCA_014858255.1_ASM1485825v1_genomic.fna.gz --refList GCA_014858255.1_ASM1485825v1_genomic.fna/target_genomes.txt --output GCA_014858255.1_ASM1485825v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:49,542] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:49,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:49,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:49,553] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2023-06-19 13:54:49,553] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 13:54:49,553] [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	97.7968	517	545	95	conclusive
Cronobacter sakazakii	strain=NBRC 102416	GCA_000684935.1	28141	28141	type	True	97.768	505	545	95	conclusive
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	97.7663	515	545	95	conclusive
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	97.7047	491	545	95	conclusive
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	94.6596	508	545	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	94.5739	504	545	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	80.5639	351	545	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	80.4647	340	545	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	80.4641	346	545	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.3383	339	545	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:54:49,555] [INFO] DFAST Taxonomy check result was written to GCA_014858255.1_ASM1485825v1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:49,556] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:49,556] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:49,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference/checkm_data
[2023-06-19 13:54:49,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:49,584] [INFO] Task started: CheckM
[2023-06-19 13:54:49,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014858255.1_ASM1485825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014858255.1_ASM1485825v1_genomic.fna/checkm_input GCA_014858255.1_ASM1485825v1_genomic.fna/checkm_result
[2023-06-19 13:55:10,137] [INFO] Task succeeded: CheckM
[2023-06-19 13:55:10,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:55:10,162] [INFO] ===== Completeness check finished =====
[2023-06-19 13:55:10,162] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:55:10,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014858255.1_ASM1485825v1_genomic.fna/markers.fasta)
[2023-06-19 13:55:10,163] [INFO] Task started: Blastn
[2023-06-19 13:55:10,163] [INFO] Running command: blastn -query GCA_014858255.1_ASM1485825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a61bbe-cf29-4f9a-886a-f2a3b596faa0/dqc_reference/reference_markers_gtdb.fasta -out GCA_014858255.1_ASM1485825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:55:11,476] [INFO] Task succeeded: Blastn
[2023-06-19 13:55:11,481] [INFO] Selected 6 target genomes.
[2023-06-19 13:55:11,481] [INFO] Target genome list was writen to GCA_014858255.1_ASM1485825v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:55:11,487] [INFO] Task started: fastANI
[2023-06-19 13:55:11,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgab5cda5d-954d-469f-a93b-1bca4abbce97/GCA_014858255.1_ASM1485825v1_genomic.fna.gz --refList GCA_014858255.1_ASM1485825v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014858255.1_ASM1485825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:55:16,411] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:16,421] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:55:16,421] [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	97.7968	517	545	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	94.6596	508	545	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	93.509	502	545	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	92.075	508	545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277195.1	s__Cronobacter muytjensii	89.4321	478	545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_001277235.1	s__Cronobacter dublinensis	89.3195	499	545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
--------------------------------------------------------------------------------
[2023-06-19 13:55:16,423] [INFO] GTDB search result was written to GCA_014858255.1_ASM1485825v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:55:16,424] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:55:16,427] [INFO] DFAST_QC result json was written to GCA_014858255.1_ASM1485825v1_genomic.fna/dqc_result.json
[2023-06-19 13:55:16,427] [INFO] DFAST_QC completed!
[2023-06-19 13:55:16,428] [INFO] Total running time: 0h0m41s