[2024-01-24 14:23:05,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:05,262] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:05,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference
[2024-01-24 14:23:06,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,574] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,574] [INFO] Running command: gunzip -c /var/lib/cwl/stge68c2b07-49c3-4e1a-b33c-f9f91b8cce6a/GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/cds.fna -a GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:15,682] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:15,683] [INFO] Task started: HMMsearch
[2024-01-24 14:23:15,683] [INFO] Running command: hmmsearch --tblout GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference/reference_markers.hmm GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:16,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:16,008] [INFO] Found 6/6 markers.
[2024-01-24 14:23:16,048] [INFO] Query marker FASTA was written to GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:23:16,048] [INFO] Task started: Blastn
[2024-01-24 14:23:16,049] [INFO] Running command: blastn -query GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference/reference_markers.fasta -out GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:16,849] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:16,852] [INFO] Selected 25 target genomes.
[2024-01-24 14:23:16,853] [INFO] Target genome list was writen to GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:23:16,862] [INFO] Task started: fastANI
[2024-01-24 14:23:16,863] [INFO] Running command: fastANI --query /var/lib/cwl/stge68c2b07-49c3-4e1a-b33c-f9f91b8cce6a/GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna.gz --refList GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:35,538] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:35,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:35,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:35,558] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:35,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:35,558] [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
Izhakiella capsodis	strain=N6PO6	GCA_900115045.1	1367852	1367852	type	True	100.0	1155	1155	95	conclusive
Izhakiella australiensis	strain=D4N98	GCA_002006995.1	1926881	1926881	type	True	82.7331	843	1155	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	78.3672	255	1155	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	78.1737	314	1155	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	78.1508	311	1155	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.0359	311	1155	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.009	304	1155	95	below_threshold
Mixta calida	strain=DSM 22759	GCA_002953215.1	665913	665913	type	True	77.9684	307	1155	95	below_threshold
Mixta calida	strain=LMG 25383	GCA_002095355.1	665913	665913	type	True	77.925	300	1155	95	below_threshold
Tatumella morbirosei	strain=LMG 23360	GCA_000757425.2	642227	642227	type	True	77.8395	168	1155	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	77.7979	322	1155	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_001277195.1	413501	413501	type	True	77.7593	218	1155	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	77.7577	318	1155	95	below_threshold
Siccibacter turicensis	strain=LMG 23730	GCA_000463155.2	357233	357233	type	True	77.7079	206	1155	95	below_threshold
Erwinia pyrifoliae	strain=DSM 12163	GCA_000026985.1	79967	79967	type	True	77.7043	270	1155	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	77.6774	248	1155	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	77.6749	216	1155	95	below_threshold
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	77.5715	89	1155	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	77.5501	83	1155	95	below_threshold
Cronobacter dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	77.4767	218	1155	95	below_threshold
Xenorhabdus indica	strain=DSM 17382	GCA_014467235.1	333964	333964	type	True	77.4032	81	1155	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	77.3623	195	1155	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	77.3285	172	1155	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	77.1546	206	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:35,560] [INFO] DFAST Taxonomy check result was written to GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:23:35,561] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:35,561] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:35,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference/checkm_data
[2024-01-24 14:23:35,562] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:35,602] [INFO] Task started: CheckM
[2024-01-24 14:23:35,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/checkm_input GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:24:07,198] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:07,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:07,220] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:07,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:07,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:24:07,221] [INFO] Task started: Blastn
[2024-01-24 14:24:07,221] [INFO] Running command: blastn -query GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f88b6f3-b46c-473d-b7b8-65a482e17c6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:08,211] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:08,215] [INFO] Selected 24 target genomes.
[2024-01-24 14:24:08,215] [INFO] Target genome list was writen to GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:08,232] [INFO] Task started: fastANI
[2024-01-24 14:24:08,232] [INFO] Running command: fastANI --query /var/lib/cwl/stge68c2b07-49c3-4e1a-b33c-f9f91b8cce6a/GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna.gz --refList GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:25,689] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:25,711] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:25,711] [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_900115045.1	s__Izhakiella capsodis	100.0	1155	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002006995.1	s__Izhakiella australiensis	82.7263	844	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752165.1	s__Izhakiella sp002752165	79.9947	545	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella	95.0	99.99	99.99	0.99	0.98	7	-
GCF_000404125.1	s__Erwinia tracheiphila	78.261	249	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.22	98.89	0.92	0.87	3	-
GCF_009914055.1	s__Mixta intestinalis	78.1516	311	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000773975.1	s__Erwinia typographi	78.1281	302	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.41	96.41	0.95	0.95	2	-
GCF_002953195.1	s__Mixta gaviniae	78.1079	310	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.91	99.91	0.99	0.99	2	-
GCF_014838825.1	s__Erwinia persicina_A	78.0655	264	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCA_019132875.1	s__Erwinia sp019132875	78.0085	304	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751505.1	s__Erwinia sp003751505	77.9903	298	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953215.1	s__Mixta calida	77.976	305	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.65	99.42	0.96	0.92	22	-
GCF_000770305.1	s__Erwinia oleae	77.9183	279	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.06	98.06	0.89	0.89	2	-
GCF_006494375.1	s__Pantoea anthophila	77.8665	261	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.39	98.21	0.92	0.90	16	-
GCF_006517625.1	s__Mixta tenebrionis	77.8064	320	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.45	99.45	0.92	0.92	2	-
GCF_001277195.1	s__Cronobacter muytjensii	77.7518	215	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_011752625.1	s__Pantoea sp011752625	77.7025	255	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095485.1	s__Pantoea wallisii	77.6898	284	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900068845.1	s__Pantoea ludwigii_A	77.6804	267	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000463155.2	s__Siccibacter turicensis	77.6781	206	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	98.74	97.87	0.95	0.92	6	-
GCF_003386665.1	s__Xenorhabdus cabanillasii	77.6013	86	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_001277235.1	s__Cronobacter dublinensis	77.4941	213	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_014467235.1	s__Xenorhabdus indica	77.4244	80	1155	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:25,713] [INFO] GTDB search result was written to GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:25,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:25,719] [INFO] DFAST_QC result json was written to GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:24:25,719] [INFO] DFAST_QC completed!
[2024-01-24 14:24:25,719] [INFO] Total running time: 0h1m20s