[2024-01-24 13:28:13,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference
[2024-01-24 13:28:14,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,575] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,576] [INFO] Running command: gunzip -c /var/lib/cwl/stgeec9928a-992c-44fe-a436-8ab903ce2cef/GCF_009738185.1_ASM973818v1_genomic.fna.gz | prodigal -d GCF_009738185.1_ASM973818v1_genomic.fna/cds.fna -a GCF_009738185.1_ASM973818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:27,309] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:27,309] [INFO] Task started: HMMsearch
[2024-01-24 13:28:27,309] [INFO] Running command: hmmsearch --tblout GCF_009738185.1_ASM973818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference/reference_markers.hmm GCF_009738185.1_ASM973818v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:27,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:27,708] [INFO] Found 6/6 markers.
[2024-01-24 13:28:27,754] [INFO] Query marker FASTA was written to GCF_009738185.1_ASM973818v1_genomic.fna/markers.fasta
[2024-01-24 13:28:27,754] [INFO] Task started: Blastn
[2024-01-24 13:28:27,755] [INFO] Running command: blastn -query GCF_009738185.1_ASM973818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference/reference_markers.fasta -out GCF_009738185.1_ASM973818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:28,804] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:28,806] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:28,807] [INFO] Target genome list was writen to GCF_009738185.1_ASM973818v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:28,814] [INFO] Task started: fastANI
[2024-01-24 13:28:28,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgeec9928a-992c-44fe-a436-8ab903ce2cef/GCF_009738185.1_ASM973818v1_genomic.fna.gz --refList GCF_009738185.1_ASM973818v1_genomic.fna/target_genomes.txt --output GCF_009738185.1_ASM973818v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:40,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:40,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:40,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:40,363] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:40,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:40,363] [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 persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	83.862	1104	1582	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	83.2106	1058	1582	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	83.0569	1051	1582	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	81.5295	752	1582	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	81.3955	781	1582	95	below_threshold
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	81.3697	752	1582	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	81.2384	785	1582	95	below_threshold
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	81.1997	754	1582	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.7221	687	1582	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.3638	614	1582	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	78.6869	461	1582	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	78.6703	354	1582	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:40,365] [INFO] DFAST Taxonomy check result was written to GCF_009738185.1_ASM973818v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:40,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:40,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:40,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference/checkm_data
[2024-01-24 13:28:40,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:40,423] [INFO] Task started: CheckM
[2024-01-24 13:28:40,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009738185.1_ASM973818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009738185.1_ASM973818v1_genomic.fna/checkm_input GCF_009738185.1_ASM973818v1_genomic.fna/checkm_result
[2024-01-24 13:29:23,381] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:23,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:23,403] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:23,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:23,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009738185.1_ASM973818v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:23,404] [INFO] Task started: Blastn
[2024-01-24 13:29:23,404] [INFO] Running command: blastn -query GCF_009738185.1_ASM973818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0a823d-1fb0-4d14-90fd-25dcdb711db3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009738185.1_ASM973818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:24,960] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:24,963] [INFO] Selected 9 target genomes.
[2024-01-24 13:29:24,964] [INFO] Target genome list was writen to GCF_009738185.1_ASM973818v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:24,978] [INFO] Task started: fastANI
[2024-01-24 13:29:24,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgeec9928a-992c-44fe-a436-8ab903ce2cef/GCF_009738185.1_ASM973818v1_genomic.fna.gz --refList GCF_009738185.1_ASM973818v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009738185.1_ASM973818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:34,847] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:34,862] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:34,862] [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_009738185.1	s__Erwinia sp009738185	100.0	1581	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.50	99.50	0.98	0.98	2	conclusive
GCF_012271765.1	s__Erwinia rhapontici	85.6892	1217	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_014838825.1	s__Erwinia persicina_A	83.9679	1155	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCF_001571305.1	s__Erwinia persicina	83.8713	1102	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.41	99.25	0.96	0.94	13	-
GCF_014773485.1	s__Erwinia aphidicola	83.0401	1054	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_016909495.1	s__Erwinia coffeiphila	81.5763	903	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.75	96.67	0.88	0.87	4	-
GCF_003751505.1	s__Erwinia sp003751505	81.5533	906	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026985.1	s__Erwinia pyrifoliae	81.52	753	1582	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	81.2351	785	1582	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:34,863] [INFO] GTDB search result was written to GCF_009738185.1_ASM973818v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:34,864] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:34,867] [INFO] DFAST_QC result json was written to GCF_009738185.1_ASM973818v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:34,867] [INFO] DFAST_QC completed!
[2024-01-24 13:29:34,868] [INFO] Total running time: 0h1m22s