[2024-01-24 12:44:41,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:41,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:41,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference
[2024-01-24 12:44:42,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:42,513] [INFO] Task started: Prodigal
[2024-01-24 12:44:42,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfeeb5c3-b58b-41bf-a20a-ffc5367b2bea/GCF_900447315.1_50465_E01_genomic.fna.gz | prodigal -d GCF_900447315.1_50465_E01_genomic.fna/cds.fna -a GCF_900447315.1_50465_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:53,838] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:53,839] [INFO] Task started: HMMsearch
[2024-01-24 12:44:53,839] [INFO] Running command: hmmsearch --tblout GCF_900447315.1_50465_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference/reference_markers.hmm GCF_900447315.1_50465_E01_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:54,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:54,181] [INFO] Found 6/6 markers.
[2024-01-24 12:44:54,225] [INFO] Query marker FASTA was written to GCF_900447315.1_50465_E01_genomic.fna/markers.fasta
[2024-01-24 12:44:54,225] [INFO] Task started: Blastn
[2024-01-24 12:44:54,226] [INFO] Running command: blastn -query GCF_900447315.1_50465_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference/reference_markers.fasta -out GCF_900447315.1_50465_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,101] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,104] [INFO] Selected 10 target genomes.
[2024-01-24 12:44:55,104] [INFO] Target genome list was writen to GCF_900447315.1_50465_E01_genomic.fna/target_genomes.txt
[2024-01-24 12:44:55,109] [INFO] Task started: fastANI
[2024-01-24 12:44:55,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfeeb5c3-b58b-41bf-a20a-ffc5367b2bea/GCF_900447315.1_50465_E01_genomic.fna.gz --refList GCF_900447315.1_50465_E01_genomic.fna/target_genomes.txt --output GCF_900447315.1_50465_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:03,717] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:03,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:03,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:03,730] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:45:03,730] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:03,730] [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
Edwardsiella hoshinae	strain=NCTC12121	GCA_900447315.1	93378	93378	type	True	100.0	1283	1289	95	conclusive
Edwardsiella hoshinae	strain=FDAARGOS_940	GCA_016026395.1	93378	93378	type	True	99.9967	1271	1289	95	conclusive
Edwardsiella hoshinae	strain=NBRC 105699	GCA_000474215.1	93378	93378	type	True	99.9542	1182	1289	95	conclusive
Edwardsiella tarda	strain=ATCC 15947	GCA_003113495.2	636	636	type	True	88.8175	1032	1289	95	below_threshold
Edwardsiella tarda	strain=NBRC 105688	GCA_000341505.1	636	636	type	True	88.6279	1014	1289	95	below_threshold
Edwardsiella tarda	strain=ATCC 15947	GCA_000264805.1	636	636	type	True	88.5898	937	1289	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.6581	401	1289	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.5404	388	1289	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.0462	243	1289	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	77.8334	265	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:03,732] [INFO] DFAST Taxonomy check result was written to GCF_900447315.1_50465_E01_genomic.fna/tc_result.tsv
[2024-01-24 12:45:03,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:03,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:03,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference/checkm_data
[2024-01-24 12:45:03,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:03,773] [INFO] Task started: CheckM
[2024-01-24 12:45:03,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447315.1_50465_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447315.1_50465_E01_genomic.fna/checkm_input GCF_900447315.1_50465_E01_genomic.fna/checkm_result
[2024-01-24 12:45:40,668] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:40,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:40,686] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:40,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:40,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447315.1_50465_E01_genomic.fna/markers.fasta)
[2024-01-24 12:45:40,687] [INFO] Task started: Blastn
[2024-01-24 12:45:40,687] [INFO] Running command: blastn -query GCF_900447315.1_50465_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg2955c764-f495-4a80-952a-1daf05bfa56b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447315.1_50465_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:41,788] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:41,813] [INFO] Selected 8 target genomes.
[2024-01-24 12:45:41,813] [INFO] Target genome list was writen to GCF_900447315.1_50465_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:41,834] [INFO] Task started: fastANI
[2024-01-24 12:45:41,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfeeb5c3-b58b-41bf-a20a-ffc5367b2bea/GCF_900447315.1_50465_E01_genomic.fna.gz --refList GCF_900447315.1_50465_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447315.1_50465_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:49,051] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:49,061] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:49,061] [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_000474215.1	s__Edwardsiella hoshinae	99.9542	1182	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	conclusive
GCF_000341505.1	s__Edwardsiella tarda	88.6279	1014	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.01	97.25	0.94	0.84	19	-
GCF_000264765.2	s__Edwardsiella anguillarum	83.5052	915	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.66	0.99	0.97	9	-
GCF_001896205.1	s__Edwardsiella piscicida	83.3592	895	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.37	99.20	0.95	0.93	23	-
GCF_000264785.1	s__Edwardsiella ictaluri	82.6033	802	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.74	99.41	0.96	0.93	11	-
GCF_000738675.1	s__Serratia nematodiphila	78.8597	420	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	98.32	97.66	0.93	0.88	85	-
GCF_002900365.1	s__Escherichia marmotae	78.7163	246	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_007680145.1	s__Pseudescherichia sp002298805	77.9206	263	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pseudescherichia	95.0	98.55	96.56	0.95	0.92	13	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:49,063] [INFO] GTDB search result was written to GCF_900447315.1_50465_E01_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:49,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:49,066] [INFO] DFAST_QC result json was written to GCF_900447315.1_50465_E01_genomic.fna/dqc_result.json
[2024-01-24 12:45:49,066] [INFO] DFAST_QC completed!
[2024-01-24 12:45:49,066] [INFO] Total running time: 0h1m8s