[2024-01-24 11:43:42,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference
[2024-01-24 11:43:43,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,651] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg67810cd3-bed0-4e1b-a8a3-a154a3090836/GCF_018494055.1_ASM1849405v1_genomic.fna.gz | prodigal -d GCF_018494055.1_ASM1849405v1_genomic.fna/cds.fna -a GCF_018494055.1_ASM1849405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:51,024] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:51,024] [INFO] Task started: HMMsearch
[2024-01-24 11:43:51,024] [INFO] Running command: hmmsearch --tblout GCF_018494055.1_ASM1849405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference/reference_markers.hmm GCF_018494055.1_ASM1849405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:51,357] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:51,358] [INFO] Found 6/6 markers.
[2024-01-24 11:43:51,386] [INFO] Query marker FASTA was written to GCF_018494055.1_ASM1849405v1_genomic.fna/markers.fasta
[2024-01-24 11:43:51,386] [INFO] Task started: Blastn
[2024-01-24 11:43:51,386] [INFO] Running command: blastn -query GCF_018494055.1_ASM1849405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference/reference_markers.fasta -out GCF_018494055.1_ASM1849405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:52,298] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:52,301] [INFO] Selected 16 target genomes.
[2024-01-24 11:43:52,301] [INFO] Target genome list was writen to GCF_018494055.1_ASM1849405v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:52,307] [INFO] Task started: fastANI
[2024-01-24 11:43:52,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg67810cd3-bed0-4e1b-a8a3-a154a3090836/GCF_018494055.1_ASM1849405v1_genomic.fna.gz --refList GCF_018494055.1_ASM1849405v1_genomic.fna/target_genomes.txt --output GCF_018494055.1_ASM1849405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:04,395] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:04,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:04,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:04,407] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:04,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:04,408] [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
Rosenbergiella epipactidis	strain=2.1A	GCA_018494055.1	1544694	1544694	type	True	100.0	1060	1060	95	conclusive
Rosenbergiella nectarea	strain=8N4	GCA_900111105.1	988801	988801	type	True	87.8433	889	1060	95	below_threshold
Rosenbergiella collisarenosi	strain=8.8A	GCA_018494085.1	1544695	1544695	type	True	82.3301	652	1060	95	below_threshold
Rosenbergiella australiborealis	strain=CdVSA20.1	GCA_018494035.1	1544696	1544696	type	True	81.4725	528	1060	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	78.4453	141	1060	95	below_threshold
Tatumella saanichensis	strain=NML 06-3099	GCA_000439375.1	480813	480813	type	True	78.4204	180	1060	95	below_threshold
Pantoea eucrina	strain=LMG 5346	GCA_002095385.1	472693	472693	type	True	78.3889	133	1060	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	78.3743	117	1060	95	below_threshold
Pantoea dispersa	strain=DSM 30073	GCA_014155765.1	59814	59814	type	True	78.2724	135	1060	95	below_threshold
Pantoea deleyi	strain=LMG 24200	GCA_002095375.1	470932	470932	type	True	78.1938	131	1060	95	below_threshold
Klebsiella aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	78.1807	98	1060	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.102	85	1060	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	77.9004	135	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:04,409] [INFO] DFAST Taxonomy check result was written to GCF_018494055.1_ASM1849405v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:04,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:04,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:04,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference/checkm_data
[2024-01-24 11:44:04,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:04,444] [INFO] Task started: CheckM
[2024-01-24 11:44:04,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018494055.1_ASM1849405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018494055.1_ASM1849405v1_genomic.fna/checkm_input GCF_018494055.1_ASM1849405v1_genomic.fna/checkm_result
[2024-01-24 11:44:33,768] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:33,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:33,790] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:33,790] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:33,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018494055.1_ASM1849405v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:33,791] [INFO] Task started: Blastn
[2024-01-24 11:44:33,791] [INFO] Running command: blastn -query GCF_018494055.1_ASM1849405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54f677a5-7dfe-46b7-ab1d-86a3a6081a80/dqc_reference/reference_markers_gtdb.fasta -out GCF_018494055.1_ASM1849405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,011] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,015] [INFO] Selected 7 target genomes.
[2024-01-24 11:44:35,015] [INFO] Target genome list was writen to GCF_018494055.1_ASM1849405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:35,022] [INFO] Task started: fastANI
[2024-01-24 11:44:35,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg67810cd3-bed0-4e1b-a8a3-a154a3090836/GCF_018494055.1_ASM1849405v1_genomic.fna.gz --refList GCF_018494055.1_ASM1849405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018494055.1_ASM1849405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:41,220] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:41,227] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:41,227] [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_018494055.1	s__Rosenbergiella epipactidis	100.0	1060	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.28	95.56	0.88	0.85	5	conclusive
GCF_900111105.1	s__Rosenbergiella nectarea	87.8433	889	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
GCF_018494065.1	s__Rosenbergiella sp018494065	84.6732	766	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018494085.1	s__Rosenbergiella collisarenosi	82.3265	653	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	99.00	99.00	0.87	0.87	2	-
GCF_018494035.1	s__Rosenbergiella australiborealis	81.4671	529	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187905.1	s__Pantoea sp001187905	78.3936	133	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_011752625.1	s__Pantoea sp011752625	78.3757	142	1060	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,229] [INFO] GTDB search result was written to GCF_018494055.1_ASM1849405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:41,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:41,236] [INFO] DFAST_QC result json was written to GCF_018494055.1_ASM1849405v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:41,237] [INFO] DFAST_QC completed!
[2024-01-24 11:44:41,237] [INFO] Total running time: 0h0m59s