[2024-01-25 20:05:20,656] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference
[2024-01-25 20:05:21,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,760] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,760] [INFO] Running command: gunzip -c /var/lib/cwl/stge254d9e3-c607-441b-99f0-b73f3dfba7ac/GCF_020097475.1_ASM2009747v1_genomic.fna.gz | prodigal -d GCF_020097475.1_ASM2009747v1_genomic.fna/cds.fna -a GCF_020097475.1_ASM2009747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:34,200] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:34,200] [INFO] Task started: HMMsearch
[2024-01-25 20:05:34,200] [INFO] Running command: hmmsearch --tblout GCF_020097475.1_ASM2009747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference/reference_markers.hmm GCF_020097475.1_ASM2009747v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:34,512] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:34,513] [INFO] Found 6/6 markers.
[2024-01-25 20:05:34,554] [INFO] Query marker FASTA was written to GCF_020097475.1_ASM2009747v1_genomic.fna/markers.fasta
[2024-01-25 20:05:34,555] [INFO] Task started: Blastn
[2024-01-25 20:05:34,555] [INFO] Running command: blastn -query GCF_020097475.1_ASM2009747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference/reference_markers.fasta -out GCF_020097475.1_ASM2009747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:35,360] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:35,363] [INFO] Selected 18 target genomes.
[2024-01-25 20:05:35,363] [INFO] Target genome list was writen to GCF_020097475.1_ASM2009747v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:35,393] [INFO] Task started: fastANI
[2024-01-25 20:05:35,394] [INFO] Running command: fastANI --query /var/lib/cwl/stge254d9e3-c607-441b-99f0-b73f3dfba7ac/GCF_020097475.1_ASM2009747v1_genomic.fna.gz --refList GCF_020097475.1_ASM2009747v1_genomic.fna/target_genomes.txt --output GCF_020097475.1_ASM2009747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:53,140] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:53,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:53,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:53,151] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:05:53,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:53,152] [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
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	100.0	1547	1548	95	conclusive
Escherichia fergusonii	strain=ATCC 35469T	GCA_000026225.1	564	564	type	True	99.9955	1545	1548	95	conclusive
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	91.0057	1118	1548	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	90.9476	1122	1548	95	below_threshold
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	90.946	1010	1548	95	below_threshold
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	90.945	1059	1548	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	90.9201	1101	1548	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	90.9073	1131	1548	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	90.8691	1080	1548	95	below_threshold
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	90.8434	1078	1548	95	below_threshold
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	90.6389	1011	1548	95	below_threshold
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	90.6094	1017	1548	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	88.2178	950	1548	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	88.1101	1046	1548	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.4359	854	1548	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.4754	327	1548	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:53,153] [INFO] DFAST Taxonomy check result was written to GCF_020097475.1_ASM2009747v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:53,155] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:53,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:53,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference/checkm_data
[2024-01-25 20:05:53,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:53,201] [INFO] Task started: CheckM
[2024-01-25 20:05:53,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097475.1_ASM2009747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097475.1_ASM2009747v1_genomic.fna/checkm_input GCF_020097475.1_ASM2009747v1_genomic.fna/checkm_result
[2024-01-25 20:06:32,291] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:32,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:32,308] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:32,308] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:32,309] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097475.1_ASM2009747v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:32,309] [INFO] Task started: Blastn
[2024-01-25 20:06:32,309] [INFO] Running command: blastn -query GCF_020097475.1_ASM2009747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eca5b35-1be3-4d03-8bdb-4bbcc0455374/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097475.1_ASM2009747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:33,386] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:33,390] [INFO] Selected 11 target genomes.
[2024-01-25 20:06:33,390] [INFO] Target genome list was writen to GCF_020097475.1_ASM2009747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:33,405] [INFO] Task started: fastANI
[2024-01-25 20:06:33,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge254d9e3-c607-441b-99f0-b73f3dfba7ac/GCF_020097475.1_ASM2009747v1_genomic.fna.gz --refList GCF_020097475.1_ASM2009747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097475.1_ASM2009747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:45,911] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:45,920] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:45,921] [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_000026225.1	s__Escherichia fergusonii	99.9955	1546	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	conclusive
GCF_003697165.2	s__Escherichia coli	90.9866	1115	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
GCF_002965065.1	s__Escherichia sp002965065	89.9422	955	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004211955.1	s__Escherichia sp004211955	89.8106	1080	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005843885.1	s__Escherichia sp005843885	89.6791	1130	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_011881725.1	s__Escherichia coli_E	89.6254	1042	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498915.1	s__Escherichia ruysiae	89.3759	1089	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_001660175.1	s__Escherichia sp001660175	89.121	1104	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_002900365.1	s__Escherichia marmotae	88.2824	1102	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_015672735.1	s__Citrobacter sp015672735	82.0546	852	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337685.1	s__Citrobacter gillenii	82.0304	858	1548	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	98.72	97.36	0.89	0.84	39	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:45,924] [INFO] GTDB search result was written to GCF_020097475.1_ASM2009747v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:45,925] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:45,928] [INFO] DFAST_QC result json was written to GCF_020097475.1_ASM2009747v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:45,928] [INFO] DFAST_QC completed!
[2024-01-25 20:06:45,928] [INFO] Total running time: 0h1m25s