[2024-01-24 13:45:48,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:48,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:48,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference
[2024-01-24 13:45:50,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:50,144] [INFO] Task started: Prodigal
[2024-01-24 13:45:50,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg87757b5c-d49f-4e75-b01c-5f676a9bb142/GCF_000439895.1_atcc_33301_v1_genomic.fna.gz | prodigal -d GCF_000439895.1_atcc_33301_v1_genomic.fna/cds.fna -a GCF_000439895.1_atcc_33301_v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:58,457] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:58,458] [INFO] Task started: HMMsearch
[2024-01-24 13:45:58,458] [INFO] Running command: hmmsearch --tblout GCF_000439895.1_atcc_33301_v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference/reference_markers.hmm GCF_000439895.1_atcc_33301_v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:58,735] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:58,736] [INFO] Found 6/6 markers.
[2024-01-24 13:45:58,770] [INFO] Query marker FASTA was written to GCF_000439895.1_atcc_33301_v1_genomic.fna/markers.fasta
[2024-01-24 13:45:58,770] [INFO] Task started: Blastn
[2024-01-24 13:45:58,770] [INFO] Running command: blastn -query GCF_000439895.1_atcc_33301_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference/reference_markers.fasta -out GCF_000439895.1_atcc_33301_v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:59,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:59,647] [INFO] Selected 11 target genomes.
[2024-01-24 13:45:59,647] [INFO] Target genome list was writen to GCF_000439895.1_atcc_33301_v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:59,660] [INFO] Task started: fastANI
[2024-01-24 13:45:59,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg87757b5c-d49f-4e75-b01c-5f676a9bb142/GCF_000439895.1_atcc_33301_v1_genomic.fna.gz --refList GCF_000439895.1_atcc_33301_v1_genomic.fna/target_genomes.txt --output GCF_000439895.1_atcc_33301_v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:09,175] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:09,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:09,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:09,186] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:09,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:09,186] [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
Tatumella ptyseos	strain=ATCC 33301	GCA_000439895.1	82987	82987	type	True	100.0	1133	1136	95	conclusive
Tatumella ptyseos	strain=ATCC 33301	GCA_000735525.1	82987	82987	type	True	99.9787	1109	1136	95	conclusive
Tatumella ptyseos	strain=NCTC11468	GCA_900478715.1	82987	82987	type	True	99.967	1135	1136	95	conclusive
Tatumella saanichensis	strain=NML 06-3099	GCA_000439375.1	480813	480813	type	True	80.4648	533	1136	95	below_threshold
Tatumella morbirosei	strain=LMG 23360	GCA_000757425.2	642227	642227	type	True	80.3377	527	1136	95	below_threshold
Tatumella citrea	strain=DSM 13699	GCA_002163585.1	53336	53336	type	True	80.2087	543	1136	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	78.1743	201	1136	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.1389	180	1136	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	78.1239	198	1136	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.0981	176	1136	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.0157	208	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:09,190] [INFO] DFAST Taxonomy check result was written to GCF_000439895.1_atcc_33301_v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:09,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:09,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:09,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference/checkm_data
[2024-01-24 13:46:09,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:09,230] [INFO] Task started: CheckM
[2024-01-24 13:46:09,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000439895.1_atcc_33301_v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000439895.1_atcc_33301_v1_genomic.fna/checkm_input GCF_000439895.1_atcc_33301_v1_genomic.fna/checkm_result
[2024-01-24 13:46:41,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:41,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:41,434] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:41,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:41,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000439895.1_atcc_33301_v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:41,435] [INFO] Task started: Blastn
[2024-01-24 13:46:41,436] [INFO] Running command: blastn -query GCF_000439895.1_atcc_33301_v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928a9786-54c6-49f4-ba04-32a9193ba8ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000439895.1_atcc_33301_v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:42,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:42,739] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:42,739] [INFO] Target genome list was writen to GCF_000439895.1_atcc_33301_v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:42,761] [INFO] Task started: fastANI
[2024-01-24 13:46:42,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg87757b5c-d49f-4e75-b01c-5f676a9bb142/GCF_000439895.1_atcc_33301_v1_genomic.fna.gz --refList GCF_000439895.1_atcc_33301_v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000439895.1_atcc_33301_v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:50,919] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:50,930] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:50,930] [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_000735525.1	s__Tatumella ptyseos	99.9787	1109	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.71	99.17	0.96	0.91	4	conclusive
GCF_018257515.1	s__Tatumella sp018257515	90.081	992	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018257575.1	s__Tatumella sp018257575	80.5948	557	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	99.64	99.52	0.95	0.93	6	-
GCF_000439375.1	s__Tatumella saanichensis	80.4613	536	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757425.2	s__Tatumella morbirosei	80.3254	526	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	95.37	95.37	0.92	0.92	2	-
GCF_002163585.1	s__Tatumella citrea	80.2193	545	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002095535.1	s__Pantoea cypripedii	78.9078	287	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.97	99.97	0.99	0.99	2	-
GCF_007833795.1	s__Pantoea dispersa_B	78.5688	278	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905795.1	s__Pantoea sp003512445	78.3064	263	1136	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	99.25	99.25	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:50,935] [INFO] GTDB search result was written to GCF_000439895.1_atcc_33301_v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:50,936] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:50,939] [INFO] DFAST_QC result json was written to GCF_000439895.1_atcc_33301_v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:50,939] [INFO] DFAST_QC completed!
[2024-01-24 13:46:50,939] [INFO] Total running time: 0h1m2s