[2024-01-24 13:28:01,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,656] [INFO] DQC Reference Directory: /var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference
[2024-01-24 13:28:03,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,045] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg27552e02-8e74-473d-88df-8f190adbed00/GCF_022602565.1_ASM2260256v1_genomic.fna.gz | prodigal -d GCF_022602565.1_ASM2260256v1_genomic.fna/cds.fna -a GCF_022602565.1_ASM2260256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:10,874] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:10,875] [INFO] Task started: HMMsearch
[2024-01-24 13:28:10,875] [INFO] Running command: hmmsearch --tblout GCF_022602565.1_ASM2260256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference/reference_markers.hmm GCF_022602565.1_ASM2260256v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:11,148] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:11,150] [INFO] Found 6/6 markers.
[2024-01-24 13:28:11,181] [INFO] Query marker FASTA was written to GCF_022602565.1_ASM2260256v1_genomic.fna/markers.fasta
[2024-01-24 13:28:11,182] [INFO] Task started: Blastn
[2024-01-24 13:28:11,182] [INFO] Running command: blastn -query GCF_022602565.1_ASM2260256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference/reference_markers.fasta -out GCF_022602565.1_ASM2260256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:11,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:11,901] [INFO] Selected 21 target genomes.
[2024-01-24 13:28:11,901] [INFO] Target genome list was writen to GCF_022602565.1_ASM2260256v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:11,922] [INFO] Task started: fastANI
[2024-01-24 13:28:11,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg27552e02-8e74-473d-88df-8f190adbed00/GCF_022602565.1_ASM2260256v1_genomic.fna.gz --refList GCF_022602565.1_ASM2260256v1_genomic.fna/target_genomes.txt --output GCF_022602565.1_ASM2260256v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:26,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:26,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:26,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:26,872] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:26,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:26,873] [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	94.6932	900	1078	95	below_threshold
Rosenbergiella nectarea	strain=8N4	GCA_900111105.1	988801	988801	type	True	86.7724	878	1078	95	below_threshold
Rosenbergiella collisarenosi	strain=8.8A	GCA_018494085.1	1544695	1544695	type	True	81.7819	621	1078	95	below_threshold
Rosenbergiella australiborealis	strain=CdVSA20.1	GCA_018494035.1	1544696	1544696	type	True	81.2627	533	1078	95	below_threshold
Pantoea stewartii subsp. indologenes	strain=LMG 2632	GCA_000757405.2	66270	66269	type	True	78.6257	142	1078	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	78.5691	86	1078	95	below_threshold
Klebsiella aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	78.55	95	1078	95	below_threshold
Pantoea rwandensis	strain=LMG 26275	GCA_002095475.1	1076550	1076550	type	True	78.4534	139	1078	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	78.4327	96	1078	95	below_threshold
Tatumella morbirosei	strain=LMG 23360	GCA_000757425.2	642227	642227	type	True	78.4064	190	1078	95	below_threshold
Pantoea allii	strain=LMG 24248	GCA_002307475.1	574096	574096	type	True	78.3945	142	1078	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	78.1856	145	1078	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	78.1636	110	1078	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	78.1001	107	1078	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	77.9253	125	1078	95	below_threshold
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	77.9176	110	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:26,875] [INFO] DFAST Taxonomy check result was written to GCF_022602565.1_ASM2260256v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:26,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:26,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:26,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference/checkm_data
[2024-01-24 13:28:26,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:26,913] [INFO] Task started: CheckM
[2024-01-24 13:28:26,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022602565.1_ASM2260256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022602565.1_ASM2260256v1_genomic.fna/checkm_input GCF_022602565.1_ASM2260256v1_genomic.fna/checkm_result
[2024-01-24 13:28:54,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:54,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:54,846] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:54,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:54,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022602565.1_ASM2260256v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:54,847] [INFO] Task started: Blastn
[2024-01-24 13:28:54,847] [INFO] Running command: blastn -query GCF_022602565.1_ASM2260256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge940543f-7b6d-4564-b504-2a94da0a6d4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_022602565.1_ASM2260256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:55,896] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:55,900] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:55,900] [INFO] Target genome list was writen to GCF_022602565.1_ASM2260256v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:55,917] [INFO] Task started: fastANI
[2024-01-24 13:28:55,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg27552e02-8e74-473d-88df-8f190adbed00/GCF_022602565.1_ASM2260256v1_genomic.fna.gz --refList GCF_022602565.1_ASM2260256v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022602565.1_ASM2260256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:04,125] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:04,137] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:04,138] [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	94.6932	900	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.28	95.56	0.88	0.85	5	-
GCF_900111105.1	s__Rosenbergiella nectarea	86.7724	878	1078	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	84.2034	762	1078	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	81.7823	618	1078	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	81.2706	534	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018257515.1	s__Tatumella sp018257515	78.0554	173	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Tatumella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187905.1	s__Pantoea sp001187905	78.0327	144	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	98.42	98.35	0.91	0.90	3	-
GCF_000773965.1	s__Pantoea cancerogena_A	77.9692	147	1078	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	96.89	96.70	0.91	0.89	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:04,140] [INFO] GTDB search result was written to GCF_022602565.1_ASM2260256v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:04,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:04,145] [INFO] DFAST_QC result json was written to GCF_022602565.1_ASM2260256v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:04,146] [INFO] DFAST_QC completed!
[2024-01-24 13:29:04,146] [INFO] Total running time: 0h1m2s