[2024-01-24 14:15:33,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:33,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:33,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference
[2024-01-24 14:15:35,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,384] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg654aa3f4-c130-40e9-b910-1f3cb1b78378/GCF_024169515.1_ASM2416951v1_genomic.fna.gz | prodigal -d GCF_024169515.1_ASM2416951v1_genomic.fna/cds.fna -a GCF_024169515.1_ASM2416951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:51,454] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:51,454] [INFO] Task started: HMMsearch
[2024-01-24 14:15:51,454] [INFO] Running command: hmmsearch --tblout GCF_024169515.1_ASM2416951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference/reference_markers.hmm GCF_024169515.1_ASM2416951v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:51,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:51,822] [INFO] Found 6/6 markers.
[2024-01-24 14:15:51,864] [INFO] Query marker FASTA was written to GCF_024169515.1_ASM2416951v1_genomic.fna/markers.fasta
[2024-01-24 14:15:51,865] [INFO] Task started: Blastn
[2024-01-24 14:15:51,865] [INFO] Running command: blastn -query GCF_024169515.1_ASM2416951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference/reference_markers.fasta -out GCF_024169515.1_ASM2416951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:52,871] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:52,879] [INFO] Selected 11 target genomes.
[2024-01-24 14:15:52,880] [INFO] Target genome list was writen to GCF_024169515.1_ASM2416951v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:52,883] [INFO] Task started: fastANI
[2024-01-24 14:15:52,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg654aa3f4-c130-40e9-b910-1f3cb1b78378/GCF_024169515.1_ASM2416951v1_genomic.fna.gz --refList GCF_024169515.1_ASM2416951v1_genomic.fna/target_genomes.txt --output GCF_024169515.1_ASM2416951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:04,302] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:04,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:04,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:04,316] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:16:04,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:04,317] [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=X001	GCA_024169515.1	68334	68334	type	True	100.0	1642	1642	95	conclusive
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	98.1198	1444	1642	95	conclusive
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	83.3179	1088	1642	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	82.1819	833	1642	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	82.0496	866	1642	95	below_threshold
Erwinia piriflorinigrans	strain=CFBP 5888	GCA_001050515.1	665097	665097	type	True	81.939	795	1642	95	below_threshold
Erwinia amylovora	strain=NBRC 12687	GCA_000696075.1	552	552	type	True	81.7575	816	1642	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	80.5604	791	1642	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.9616	794	1642	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.5051	687	1642	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	78.8778	555	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:04,319] [INFO] DFAST Taxonomy check result was written to GCF_024169515.1_ASM2416951v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:04,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:04,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:04,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference/checkm_data
[2024-01-24 14:16:04,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:04,369] [INFO] Task started: CheckM
[2024-01-24 14:16:04,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024169515.1_ASM2416951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024169515.1_ASM2416951v1_genomic.fna/checkm_input GCF_024169515.1_ASM2416951v1_genomic.fna/checkm_result
[2024-01-24 14:16:53,792] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:53,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:53,813] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:53,814] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:53,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024169515.1_ASM2416951v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:53,815] [INFO] Task started: Blastn
[2024-01-24 14:16:53,815] [INFO] Running command: blastn -query GCF_024169515.1_ASM2416951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e369129-8344-4dac-a5ed-8355dc6de7a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024169515.1_ASM2416951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:55,386] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:55,391] [INFO] Selected 10 target genomes.
[2024-01-24 14:16:55,391] [INFO] Target genome list was writen to GCF_024169515.1_ASM2416951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:55,400] [INFO] Task started: fastANI
[2024-01-24 14:16:55,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg654aa3f4-c130-40e9-b910-1f3cb1b78378/GCF_024169515.1_ASM2416951v1_genomic.fna.gz --refList GCF_024169515.1_ASM2416951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024169515.1_ASM2416951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:07,413] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:07,426] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:07,426] [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	98.114	1446	1642	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	92.5194	383	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.47	98.24	0.66	0.61	4	-
GCF_012271765.1	s__Erwinia rhapontici	83.5226	1122	1642	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	83.4243	1114	1642	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	83.3085	1091	1642	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	83.22	1056	1642	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	82.919	1053	1642	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	82.5587	994	1642	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	82.1821	835	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.33	98.13	0.97	0.93	4	-
GCF_009765445.1	s__Erwinia sp009765445	81.2564	900	1642	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 14:17:07,427] [INFO] GTDB search result was written to GCF_024169515.1_ASM2416951v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:07,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:07,431] [INFO] DFAST_QC result json was written to GCF_024169515.1_ASM2416951v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:07,431] [INFO] DFAST_QC completed!
[2024-01-24 14:17:07,432] [INFO] Total running time: 0h1m34s