[2024-01-24 12:22:18,490] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:18,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:18,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference
[2024-01-24 12:22:19,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:19,772] [INFO] Task started: Prodigal
[2024-01-24 12:22:19,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c5d7bd5-df89-4318-b05e-ef328fe70b39/GCF_000367625.1_ASM36762v2_genomic.fna.gz | prodigal -d GCF_000367625.1_ASM36762v2_genomic.fna/cds.fna -a GCF_000367625.1_ASM36762v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:30,057] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:30,057] [INFO] Task started: HMMsearch
[2024-01-24 12:22:30,057] [INFO] Running command: hmmsearch --tblout GCF_000367625.1_ASM36762v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference/reference_markers.hmm GCF_000367625.1_ASM36762v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:30,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:30,338] [INFO] Found 6/6 markers.
[2024-01-24 12:22:30,375] [INFO] Query marker FASTA was written to GCF_000367625.1_ASM36762v2_genomic.fna/markers.fasta
[2024-01-24 12:22:30,375] [INFO] Task started: Blastn
[2024-01-24 12:22:30,376] [INFO] Running command: blastn -query GCF_000367625.1_ASM36762v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference/reference_markers.fasta -out GCF_000367625.1_ASM36762v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:31,359] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:31,363] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:31,364] [INFO] Target genome list was writen to GCF_000367625.1_ASM36762v2_genomic.fna/target_genomes.txt
[2024-01-24 12:22:31,369] [INFO] Task started: fastANI
[2024-01-24 12:22:31,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c5d7bd5-df89-4318-b05e-ef328fe70b39/GCF_000367625.1_ASM36762v2_genomic.fna.gz --refList GCF_000367625.1_ASM36762v2_genomic.fna/target_genomes.txt --output GCF_000367625.1_ASM36762v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:42,911] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:42,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:42,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:42,923] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:42,924] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:42,924] [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
Erwinia amylovora	strain=type strain: CFBP 1232	GCA_000367625.2	552	552	type	True	100.0	1242	1246	95	conclusive
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	99.9912	1246	1246	95	conclusive
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	99.9822	1220	1246	95	conclusive
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	90.6857	1075	1246	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	85.67	969	1246	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	85.2339	976	1246	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	81.945	818	1246	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	81.8695	809	1246	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.754	552	1246	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.6889	353	1246	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.6838	410	1246	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	78.4385	349	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,925] [INFO] DFAST Taxonomy check result was written to GCF_000367625.1_ASM36762v2_genomic.fna/tc_result.tsv
[2024-01-24 12:22:42,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:42,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:42,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference/checkm_data
[2024-01-24 12:22:42,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:42,966] [INFO] Task started: CheckM
[2024-01-24 12:22:42,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367625.1_ASM36762v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367625.1_ASM36762v2_genomic.fna/checkm_input GCF_000367625.1_ASM36762v2_genomic.fna/checkm_result
[2024-01-24 12:23:18,248] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:18,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:18,265] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:18,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:18,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367625.1_ASM36762v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:18,266] [INFO] Task started: Blastn
[2024-01-24 12:23:18,266] [INFO] Running command: blastn -query GCF_000367625.1_ASM36762v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5013fd1-54b4-4be5-a4e6-07c1d5ef9746/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367625.1_ASM36762v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,656] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,660] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:19,660] [INFO] Target genome list was writen to GCF_000367625.1_ASM36762v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:19,678] [INFO] Task started: fastANI
[2024-01-24 12:23:19,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c5d7bd5-df89-4318-b05e-ef328fe70b39/GCF_000367625.1_ASM36762v2_genomic.fna.gz --refList GCF_000367625.1_ASM36762v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000367625.1_ASM36762v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:28,214] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:28,232] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:28,232] [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_017161565.1	s__Erwinia amylovora	99.9912	1246	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.73	98.13	0.99	0.95	141	conclusive
GCF_000026985.1	s__Erwinia pyrifoliae	90.6923	1074	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.33	98.13	0.97	0.93	4	-
GCF_001050515.1	s__Erwinia piriflorinigrans	85.6701	969	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026185.1	s__Erwinia tasmaniensis	85.2337	976	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001756855.1	s__Erwinia dacicola	82.1458	305	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_014773485.1	s__Erwinia aphidicola	81.8832	808	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_012271765.1	s__Erwinia rhapontici	81.3399	746	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_003751505.1	s__Erwinia sp003751505	80.9845	670	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141005.1	s__Erwinia sp001422605	80.8407	679	1246	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:28,235] [INFO] GTDB search result was written to GCF_000367625.1_ASM36762v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:28,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:28,241] [INFO] DFAST_QC result json was written to GCF_000367625.1_ASM36762v2_genomic.fna/dqc_result.json
[2024-01-24 12:23:28,241] [INFO] DFAST_QC completed!
[2024-01-24 12:23:28,241] [INFO] Total running time: 0h1m10s