[2024-01-25 17:47:05,425] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:05,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:05,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference
[2024-01-25 17:47:06,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:06,549] [INFO] Task started: Prodigal
[2024-01-25 17:47:06,549] [INFO] Running command: gunzip -c /var/lib/cwl/stge21fba66-8ab2-4acb-b987-72421463c4c3/GCF_002900365.1_ASM290036v1_genomic.fna.gz | prodigal -d GCF_002900365.1_ASM290036v1_genomic.fna/cds.fna -a GCF_002900365.1_ASM290036v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:18,151] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:18,151] [INFO] Task started: HMMsearch
[2024-01-25 17:47:18,151] [INFO] Running command: hmmsearch --tblout GCF_002900365.1_ASM290036v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference/reference_markers.hmm GCF_002900365.1_ASM290036v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:18,441] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:18,443] [INFO] Found 6/6 markers.
[2024-01-25 17:47:18,483] [INFO] Query marker FASTA was written to GCF_002900365.1_ASM290036v1_genomic.fna/markers.fasta
[2024-01-25 17:47:18,484] [INFO] Task started: Blastn
[2024-01-25 17:47:18,484] [INFO] Running command: blastn -query GCF_002900365.1_ASM290036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference/reference_markers.fasta -out GCF_002900365.1_ASM290036v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:19,275] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:19,279] [INFO] Selected 18 target genomes.
[2024-01-25 17:47:19,279] [INFO] Target genome list was writen to GCF_002900365.1_ASM290036v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:19,296] [INFO] Task started: fastANI
[2024-01-25 17:47:19,296] [INFO] Running command: fastANI --query /var/lib/cwl/stge21fba66-8ab2-4acb-b987-72421463c4c3/GCF_002900365.1_ASM290036v1_genomic.fna.gz --refList GCF_002900365.1_ASM290036v1_genomic.fna/target_genomes.txt --output GCF_002900365.1_ASM290036v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:47,521] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:47,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:47,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:47,533] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:47:47,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:47,533] [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 marmotae	strain=HT073016	GCA_002900365.1	1499973	1499973	type	True	100.0	1622	1631	95	conclusive
Escherichia marmotae	strain=HT073016	GCA_000807695.3	1499973	1499973	type	True	99.903	1434	1631	95	conclusive
Escherichia coli	strain=DSM 30083	GCA_024519395.1	562	562	neotype	True	91.0633	1263	1631	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_003697165.2	562	562	neotype	True	91.0389	1266	1631	95	below_threshold
Escherichia coli	strain=DSM 30083	GCA_000690815.1	562	562	neotype	True	90.9874	1287	1631	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	90.9656	1238	1631	95	below_threshold
Shigella sonnei	strain=NCTC12984	GCA_900457155.1	624	624	type	True	90.9074	1231	1631	95	below_threshold
Escherichia coli	strain=ATCC 11775	GCA_000734955.1	562	562	neotype	True	90.9054	1270	1631	95	below_threshold
Shigella boydii	strain=FDAARGOS_1139	GCA_016726285.1	621	621	type	True	90.9044	1171	1631	95	below_threshold
Shigella boydii	strain=NCTC12985	GCA_900457095.1	621	621	type	True	90.813	1162	1631	95	below_threshold
Shigella dysenteriae	strain=ATCC 13313	GCA_002949675.1	622	622	suspected-type	True	90.6442	1137	1631	95	below_threshold
Shigella dysenteriae	strain=NCTC4837	GCA_900457215.1	622	622	suspected-type	True	90.6197	1146	1631	95	below_threshold
Escherichia albertii	strain=NBRC 107761	GCA_000759775.1	208962	208962	type	True	89.4142	1098	1631	95	below_threshold
Escherichia albertii	strain=DSM 17582	GCA_022833075.1	208962	208962	type	True	89.3609	1182	1631	95	below_threshold
Escherichia fergusonii	strain=ATCC 35469T	GCA_000026225.1	564	564	type	True	88.5438	1091	1631	95	below_threshold
Escherichia fergusonii	strain=FDAARGOS_1499	GCA_020097475.1	564	564	type	True	88.4643	1115	1631	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.6475	834	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:47,535] [INFO] DFAST Taxonomy check result was written to GCF_002900365.1_ASM290036v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:47,535] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:47,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:47,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference/checkm_data
[2024-01-25 17:47:47,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:47,582] [INFO] Task started: CheckM
[2024-01-25 17:47:47,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002900365.1_ASM290036v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002900365.1_ASM290036v1_genomic.fna/checkm_input GCF_002900365.1_ASM290036v1_genomic.fna/checkm_result
[2024-01-25 17:48:24,539] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:24,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:24,578] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:24,578] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:24,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002900365.1_ASM290036v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:24,579] [INFO] Task started: Blastn
[2024-01-25 17:48:24,579] [INFO] Running command: blastn -query GCF_002900365.1_ASM290036v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57e2cad2-0e3e-46fc-a74b-52e2b613eb0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002900365.1_ASM290036v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:25,674] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:25,677] [INFO] Selected 11 target genomes.
[2024-01-25 17:48:25,677] [INFO] Target genome list was writen to GCF_002900365.1_ASM290036v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:25,696] [INFO] Task started: fastANI
[2024-01-25 17:48:25,696] [INFO] Running command: fastANI --query /var/lib/cwl/stge21fba66-8ab2-4acb-b987-72421463c4c3/GCF_002900365.1_ASM290036v1_genomic.fna.gz --refList GCF_002900365.1_ASM290036v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002900365.1_ASM290036v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:39,937] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:39,955] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:39,955] [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_002900365.1	s__Escherichia marmotae	100.0	1626	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.02	98.77	0.90	0.85	82	conclusive
GCF_902498915.1	s__Escherichia ruysiae	92.0978	1315	1631	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	91.4153	1332	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_001660175.1	s__Escherichia sp001660175	91.2134	1283	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	99.53	99.22	0.94	0.92	3	-
GCF_003697165.2	s__Escherichia coli	91.0454	1266	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
GCF_004211955.1	s__Escherichia sp004211955	90.9723	1253	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011881725.1	s__Escherichia coli_E	90.6304	1193	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002965065.1	s__Escherichia sp002965065	90.1182	1102	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000026225.1	s__Escherichia fergusonii	88.5554	1090	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_000474215.1	s__Edwardsiella hoshinae	77.6668	221	1631	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:39,956] [INFO] GTDB search result was written to GCF_002900365.1_ASM290036v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:39,957] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:39,960] [INFO] DFAST_QC result json was written to GCF_002900365.1_ASM290036v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:39,960] [INFO] DFAST_QC completed!
[2024-01-25 17:48:39,960] [INFO] Total running time: 0h1m35s