[2024-01-24 12:44:09,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:09,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:09,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference
[2024-01-24 12:44:11,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,020] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg968a42cb-c205-458d-a6e5-fb161e0e1e61/GCF_014773485.1_ASM1477348v1_genomic.fna.gz | prodigal -d GCF_014773485.1_ASM1477348v1_genomic.fna/cds.fna -a GCF_014773485.1_ASM1477348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:26,390] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:26,391] [INFO] Task started: HMMsearch
[2024-01-24 12:44:26,391] [INFO] Running command: hmmsearch --tblout GCF_014773485.1_ASM1477348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference/reference_markers.hmm GCF_014773485.1_ASM1477348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:26,775] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:26,776] [INFO] Found 6/6 markers.
[2024-01-24 12:44:26,822] [INFO] Query marker FASTA was written to GCF_014773485.1_ASM1477348v1_genomic.fna/markers.fasta
[2024-01-24 12:44:26,822] [INFO] Task started: Blastn
[2024-01-24 12:44:26,822] [INFO] Running command: blastn -query GCF_014773485.1_ASM1477348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference/reference_markers.fasta -out GCF_014773485.1_ASM1477348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:27,770] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:27,774] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:27,775] [INFO] Target genome list was writen to GCF_014773485.1_ASM1477348v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:27,780] [INFO] Task started: fastANI
[2024-01-24 12:44:27,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg968a42cb-c205-458d-a6e5-fb161e0e1e61/GCF_014773485.1_ASM1477348v1_genomic.fna.gz --refList GCF_014773485.1_ASM1477348v1_genomic.fna/target_genomes.txt --output GCF_014773485.1_ASM1477348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:41,863] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:41,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:41,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:41,880] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:41,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:41,881] [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 aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	100.0	1634	1691	95	conclusive
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	98.13	1440	1691	95	conclusive
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	83.2632	1075	1691	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	82.1142	820	1691	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	81.8992	850	1691	95	below_threshold
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	81.8395	810	1691	95	below_threshold
Erwinia amylovora	strain=ATCC 15580	GCA_017161565.1	552	552	type	True	81.8159	817	1691	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	81.7535	809	1691	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	80.5281	797	1691	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	80.1379	797	1691	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.8261	774	1691	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.2729	671	1691	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.8505	518	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:41,882] [INFO] DFAST Taxonomy check result was written to GCF_014773485.1_ASM1477348v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:41,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:41,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:41,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference/checkm_data
[2024-01-24 12:44:41,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:41,939] [INFO] Task started: CheckM
[2024-01-24 12:44:41,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773485.1_ASM1477348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773485.1_ASM1477348v1_genomic.fna/checkm_input GCF_014773485.1_ASM1477348v1_genomic.fna/checkm_result
[2024-01-24 12:45:30,228] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:30,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:30,253] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:30,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:30,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773485.1_ASM1477348v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:30,254] [INFO] Task started: Blastn
[2024-01-24 12:45:30,254] [INFO] Running command: blastn -query GCF_014773485.1_ASM1477348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928b881d-5c6d-423e-95b8-25c8fe304562/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773485.1_ASM1477348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:31,461] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:31,465] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:31,466] [INFO] Target genome list was writen to GCF_014773485.1_ASM1477348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:31,489] [INFO] Task started: fastANI
[2024-01-24 12:45:31,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg968a42cb-c205-458d-a6e5-fb161e0e1e61/GCF_014773485.1_ASM1477348v1_genomic.fna.gz --refList GCF_014773485.1_ASM1477348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773485.1_ASM1477348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:43,133] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:43,146] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:43,146] [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_014773485.1	s__Erwinia aphidicola	100.0	1631	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	conclusive
GCF_001756855.1	s__Erwinia dacicola	92.8034	365	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_014838825.1	s__Erwinia persicina_A	83.534	1102	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCF_012271765.1	s__Erwinia rhapontici	83.4635	1116	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_001571305.1	s__Erwinia persicina	83.2535	1076	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.41	99.25	0.96	0.94	13	-
GCF_009738185.1	s__Erwinia sp009738185	83.0631	1067	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.50	99.50	0.98	0.98	2	-
GCF_018141005.1	s__Erwinia sp001422605	82.9317	1010	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.39	98.36	0.92	0.92	3	-
GCF_016909495.1	s__Erwinia coffeiphila	82.6398	963	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.75	96.67	0.88	0.87	4	-
GCF_000026985.1	s__Erwinia pyrifoliae	82.0826	824	1691	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	81.749	810	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196615.1	s__Erwinia billingiae	81.3782	949	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	97.77	97.43	0.91	0.82	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:43,150] [INFO] GTDB search result was written to GCF_014773485.1_ASM1477348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:43,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:43,157] [INFO] DFAST_QC result json was written to GCF_014773485.1_ASM1477348v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:43,157] [INFO] DFAST_QC completed!
[2024-01-24 12:45:43,158] [INFO] Total running time: 0h1m33s