[2024-01-24 12:40:07,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference
[2024-01-24 12:40:08,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,849] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dd7444c-0a85-4fdb-932d-86d5ef470851/GCF_000406125.1_DXY569_1.0_genomic.fna.gz | prodigal -d GCF_000406125.1_DXY569_1.0_genomic.fna/cds.fna -a GCF_000406125.1_DXY569_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:21,816] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:21,817] [INFO] Task started: HMMsearch
[2024-01-24 12:40:21,817] [INFO] Running command: hmmsearch --tblout GCF_000406125.1_DXY569_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference/reference_markers.hmm GCF_000406125.1_DXY569_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:22,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:22,045] [INFO] Found 6/6 markers.
[2024-01-24 12:40:22,079] [INFO] Query marker FASTA was written to GCF_000406125.1_DXY569_1.0_genomic.fna/markers.fasta
[2024-01-24 12:40:22,079] [INFO] Task started: Blastn
[2024-01-24 12:40:22,080] [INFO] Running command: blastn -query GCF_000406125.1_DXY569_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference/reference_markers.fasta -out GCF_000406125.1_DXY569_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:22,925] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:22,928] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:22,928] [INFO] Target genome list was writen to GCF_000406125.1_DXY569_1.0_genomic.fna/target_genomes.txt
[2024-01-24 12:40:22,934] [INFO] Task started: fastANI
[2024-01-24 12:40:22,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dd7444c-0a85-4fdb-932d-86d5ef470851/GCF_000406125.1_DXY569_1.0_genomic.fna.gz --refList GCF_000406125.1_DXY569_1.0_genomic.fna/target_genomes.txt --output GCF_000406125.1_DXY569_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:41,331] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:41,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:41,346] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:41,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:41,346] [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
Dickeya poaceiphila	strain=NCPPB 569	GCA_000406125.1	568768	568768	type	True	100.0	1405	1405	95	conclusive
Dickeya poaceiphila	strain=NCPPB 569	GCA_007858975.2	568768	568768	type	True	99.9275	1398	1405	95	conclusive
Dickeya dadantii	strain=NCPPB 898	GCA_000406145.1	204038	204038	type	True	86.4695	1095	1405	95	below_threshold
Dickeya dadantii	strain=DSM 18020	GCA_003049785.1	204038	204038	type	True	86.4419	1127	1405	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	86.407	1130	1405	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	86.3999	1114	1405	95	below_threshold
Dickeya chrysanthemi	strain=NCPPB 402	GCA_000406105.1	556	556	type	True	86.3573	1106	1405	95	below_threshold
Dickeya fangzhongdai	strain=DSM 101947	GCA_002812485.1	1778540	1778540	type	True	86.3533	1144	1405	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	86.3312	1103	1405	95	below_threshold
Dickeya oryzae	strain=ZYY5	GCA_009372235.1	1240404	1240404	type	True	86.275	1098	1405	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	86.221	1121	1405	95	below_threshold
Dickeya parazeae	strain=S31	GCA_017897605.1	2893572	2893572	type	True	86.0653	1132	1405	95	below_threshold
Dickeya zeae	strain=NCPPB 2538	GCA_000406165.1	204042	204042	type	True	86.0367	1116	1405	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	80.694	717	1405	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.3184	480	1405	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.7641	435	1405	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.6348	403	1405	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.5856	423	1405	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	78.2723	320	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,348] [INFO] DFAST Taxonomy check result was written to GCF_000406125.1_DXY569_1.0_genomic.fna/tc_result.tsv
[2024-01-24 12:40:41,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:41,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:41,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference/checkm_data
[2024-01-24 12:40:41,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:41,390] [INFO] Task started: CheckM
[2024-01-24 12:40:41,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000406125.1_DXY569_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000406125.1_DXY569_1.0_genomic.fna/checkm_input GCF_000406125.1_DXY569_1.0_genomic.fna/checkm_result
[2024-01-24 12:41:21,407] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:21,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:21,423] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:21,423] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:21,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000406125.1_DXY569_1.0_genomic.fna/markers.fasta)
[2024-01-24 12:41:21,424] [INFO] Task started: Blastn
[2024-01-24 12:41:21,424] [INFO] Running command: blastn -query GCF_000406125.1_DXY569_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed7cb0e-128f-498f-9633-a9e357022c51/dqc_reference/reference_markers_gtdb.fasta -out GCF_000406125.1_DXY569_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:22,439] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:22,442] [INFO] Selected 10 target genomes.
[2024-01-24 12:41:22,442] [INFO] Target genome list was writen to GCF_000406125.1_DXY569_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:22,475] [INFO] Task started: fastANI
[2024-01-24 12:41:22,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dd7444c-0a85-4fdb-932d-86d5ef470851/GCF_000406125.1_DXY569_1.0_genomic.fna.gz --refList GCF_000406125.1_DXY569_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000406125.1_DXY569_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:33,474] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:33,481] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:33,482] [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_007858975.2	s__Dickeya poaceiphila	99.9275	1398	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.40	98.88	0.98	0.96	3	conclusive
GCF_000406145.1	s__Dickeya dadantii	86.4587	1096	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.21	96.30	0.92	0.86	14	-
GCF_000365305.1	s__Dickeya dianthicola	86.3831	1096	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.46	97.48	0.95	0.91	50	-
GCF_000406105.1	s__Dickeya chrysanthemi	86.3622	1106	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	96.33	96.25	0.88	0.87	6	-
GCF_002812485.1	s__Dickeya fangzhongdai	86.3504	1144	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	98.62	96.33	0.95	0.90	15	-
GCF_001644705.1	s__Dickeya solani	86.3418	1102	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	99.95	98.75	1.00	0.95	38	-
GCF_009372235.1	s__Dickeya oryzae	86.2745	1098	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.59	96.04	0.90	0.83	10	-
GCF_000406165.1	s__Dickeya zeae	86.0241	1118	1405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Dickeya	95.0	97.51	96.16	0.94	0.92	9	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:33,484] [INFO] GTDB search result was written to GCF_000406125.1_DXY569_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:33,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:33,487] [INFO] DFAST_QC result json was written to GCF_000406125.1_DXY569_1.0_genomic.fna/dqc_result.json
[2024-01-24 12:41:33,488] [INFO] DFAST_QC completed!
[2024-01-24 12:41:33,488] [INFO] Total running time: 0h1m26s