[2023-06-28 18:41:06,536] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:06,538] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:06,538] [INFO] DQC Reference Directory: /var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference
[2023-06-28 18:41:07,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:07,853] [INFO] Task started: Prodigal
[2023-06-28 18:41:07,854] [INFO] Running command: gunzip -c /var/lib/cwl/stga81b99d4-452d-4134-ae59-1a9ee7869640/GCA_019012525.1_ASM1901252v1_genomic.fna.gz | prodigal -d GCA_019012525.1_ASM1901252v1_genomic.fna/cds.fna -a GCA_019012525.1_ASM1901252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:19,975] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:19,975] [INFO] Task started: HMMsearch
[2023-06-28 18:41:19,976] [INFO] Running command: hmmsearch --tblout GCA_019012525.1_ASM1901252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference/reference_markers.hmm GCA_019012525.1_ASM1901252v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:20,292] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:20,293] [INFO] Found 6/6 markers.
[2023-06-28 18:41:20,333] [INFO] Query marker FASTA was written to GCA_019012525.1_ASM1901252v1_genomic.fna/markers.fasta
[2023-06-28 18:41:20,333] [INFO] Task started: Blastn
[2023-06-28 18:41:20,333] [INFO] Running command: blastn -query GCA_019012525.1_ASM1901252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference/reference_markers.fasta -out GCA_019012525.1_ASM1901252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:21,185] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:21,190] [INFO] Selected 18 target genomes.
[2023-06-28 18:41:21,190] [INFO] Target genome list was writen to GCA_019012525.1_ASM1901252v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:21,192] [INFO] Task started: fastANI
[2023-06-28 18:41:21,192] [INFO] Running command: fastANI --query /var/lib/cwl/stga81b99d4-452d-4134-ae59-1a9ee7869640/GCA_019012525.1_ASM1901252v1_genomic.fna.gz --refList GCA_019012525.1_ASM1901252v1_genomic.fna/target_genomes.txt --output GCA_019012525.1_ASM1901252v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:40,306] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:40,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:40,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:40,323] [WARNING] Following organisms are indistinguishable with ANI. [Escherichia coli(562), Shigella boydii(621), Shigella dysenteriae(622), Shigella flexneri(623), Shigella sonnei(624)]
[2023-06-28 18:41:40,324] [INFO] Found 15 fastANI hits (9 hits with ANI > threshold)
[2023-06-28 18:41:40,324] [INFO] The taxonomy check result is classified as 'indistinguishable'.
[2023-06-28 18:41:40,324] [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 coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	98.8331	1400	1524	95	indistinguishable
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	98.7616	1419	1524	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	98.7463	1421	1524	95	indistinguishable
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	98.4245	1388	1524	95	indistinguishable
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	96.5519	1240	1524	95	indistinguishable
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	96.5491	1238	1524	95	indistinguishable
Shigella flexneri 2a	strain=ATCC 29903	GCA_002950215.1	42897	623	type	True	96.4725	1219	1524	95	indistinguishable
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	96.3326	1178	1524	95	indistinguishable
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	96.0868	1151	1524	95	indistinguishable
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	90.2184	1082	1524	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.9742	1176	1524	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	82.6064	911	1524	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	82.2789	877	1524	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	78.4559	343	1524	95	below_threshold
Leminorella richardii	strain=NCTC12151	GCA_900478135.1	158841	158841	type	True	77.6935	182	1524	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:41:40,326] [INFO] DFAST Taxonomy check result was written to GCA_019012525.1_ASM1901252v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:40,327] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:40,327] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:40,327] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference/checkm_data
[2023-06-28 18:41:40,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:40,374] [INFO] Task started: CheckM
[2023-06-28 18:41:40,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019012525.1_ASM1901252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019012525.1_ASM1901252v1_genomic.fna/checkm_input GCA_019012525.1_ASM1901252v1_genomic.fna/checkm_result
[2023-06-28 18:42:19,685] [INFO] Task succeeded: CheckM
[2023-06-28 18:42:19,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:42:19,709] [INFO] ===== Completeness check finished =====
[2023-06-28 18:42:19,710] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:42:19,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019012525.1_ASM1901252v1_genomic.fna/markers.fasta)
[2023-06-28 18:42:19,710] [INFO] Task started: Blastn
[2023-06-28 18:42:19,711] [INFO] Running command: blastn -query GCA_019012525.1_ASM1901252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefaf1cf8-3ba6-4142-9456-78ec27a9438a/dqc_reference/reference_markers_gtdb.fasta -out GCA_019012525.1_ASM1901252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:42:20,805] [INFO] Task succeeded: Blastn
[2023-06-28 18:42:20,810] [INFO] Selected 15 target genomes.
[2023-06-28 18:42:20,811] [INFO] Target genome list was writen to GCA_019012525.1_ASM1901252v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:42:20,817] [INFO] Task started: fastANI
[2023-06-28 18:42:20,817] [INFO] Running command: fastANI --query /var/lib/cwl/stga81b99d4-452d-4134-ae59-1a9ee7869640/GCA_019012525.1_ASM1901252v1_genomic.fna.gz --refList GCA_019012525.1_ASM1901252v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019012525.1_ASM1901252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:42:36,709] [INFO] Task succeeded: fastANI
[2023-06-28 18:42:36,730] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:42:36,730] [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_003697165.2	s__Escherichia coli	98.7633	1419	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	conclusive
GCF_002965065.1	s__Escherichia sp002965065	94.2473	1105	1524	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	92.7823	1218	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902498915.1	s__Escherichia ruysiae	92.7319	1244	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.82	96.45	0.94	0.86	36	-
GCF_005843885.1	s__Escherichia sp005843885	92.7183	1263	1524	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	92.1871	1159	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660175.1	s__Escherichia sp001660175	91.7817	1267	1524	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	91.0203	1250	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	-
GCF_000026225.1	s__Escherichia fergusonii	90.937	1067	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_000759775.1	s__Escherichia albertii	90.2064	1082	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.47	97.95	0.90	0.82	107	-
GCF_000759815.1	s__Citrobacter_A rodentium	82.685	883	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	-
GCF_000155975.1	s__Citrobacter portucalensis_A	82.6352	942	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005281345.1	s__Citrobacter sp005281345	82.2013	905	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.53	97.53	0.86	0.86	2	-
GCF_902706235.1	s__Scandinavium sp902706235	80.9007	728	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003818135.1	s__Buttiauxella warmboldiae	79.6717	566	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:42:36,732] [INFO] GTDB search result was written to GCA_019012525.1_ASM1901252v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:42:36,734] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:42:36,738] [INFO] DFAST_QC result json was written to GCA_019012525.1_ASM1901252v1_genomic.fna/dqc_result.json
[2023-06-28 18:42:36,739] [INFO] DFAST_QC completed!
[2023-06-28 18:42:36,739] [INFO] Total running time: 0h1m30s