[2024-01-24 11:30:49,383] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference
[2024-01-24 11:30:50,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,620] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg74228a00-eb1d-4274-b85b-3681ffc5ed5b/GCF_001277175.1_ASM127717v1_genomic.fna.gz | prodigal -d GCF_001277175.1_ASM127717v1_genomic.fna/cds.fna -a GCF_001277175.1_ASM127717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:03,015] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:03,015] [INFO] Task started: HMMsearch
[2024-01-24 11:31:03,016] [INFO] Running command: hmmsearch --tblout GCF_001277175.1_ASM127717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference/reference_markers.hmm GCF_001277175.1_ASM127717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:03,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:03,295] [INFO] Found 6/6 markers.
[2024-01-24 11:31:03,332] [INFO] Query marker FASTA was written to GCF_001277175.1_ASM127717v1_genomic.fna/markers.fasta
[2024-01-24 11:31:03,333] [INFO] Task started: Blastn
[2024-01-24 11:31:03,333] [INFO] Running command: blastn -query GCF_001277175.1_ASM127717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference/reference_markers.fasta -out GCF_001277175.1_ASM127717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:04,222] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:04,226] [INFO] Selected 12 target genomes.
[2024-01-24 11:31:04,227] [INFO] Target genome list was writen to GCF_001277175.1_ASM127717v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:04,846] [INFO] Task started: fastANI
[2024-01-24 11:31:04,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg74228a00-eb1d-4274-b85b-3681ffc5ed5b/GCF_001277175.1_ASM127717v1_genomic.fna.gz --refList GCF_001277175.1_ASM127717v1_genomic.fna/target_genomes.txt --output GCF_001277175.1_ASM127717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:17,427] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:17,427] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:17,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:17,446] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:31:17,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:17,447] [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
Cronobacter universalis	strain=NCTC 9529	GCA_001277175.1	535744	535744	type	True	100.0	1478	1478	95	conclusive
Cronobacter universalis	strain=NCTC 9529	GCA_900447325.1	535744	535744	type	True	99.9978	1477	1478	95	conclusive
Cronobacter universalis	strain=NCTC 9529	GCA_000409325.1	535744	535744	type	True	99.9806	1431	1478	95	conclusive
Cronobacter universalis	strain=NCTC 9529	GCA_000319325.1	535744	535744	type	True	99.607	1448	1478	95	conclusive
Cronobacter malonaticus	strain=LMG 23826	GCA_001277215.2	413503	413503	type	True	94.2408	1355	1478	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	94.1952	1291	1478	95	below_threshold
Cronobacter sakazakii	strain=FDAARGOS_927	GCA_016103025.1	28141	28141	type	True	93.6937	1312	1478	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	93.6364	1189	1478	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.3808	841	1478	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.2518	828	1478	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	81.2443	853	1478	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.8717	836	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:17,448] [INFO] DFAST Taxonomy check result was written to GCF_001277175.1_ASM127717v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:17,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:17,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:17,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference/checkm_data
[2024-01-24 11:31:17,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:17,496] [INFO] Task started: CheckM
[2024-01-24 11:31:17,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001277175.1_ASM127717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001277175.1_ASM127717v1_genomic.fna/checkm_input GCF_001277175.1_ASM127717v1_genomic.fna/checkm_result
[2024-01-24 11:31:56,318] [INFO] Task succeeded: CheckM
[2024-01-24 11:31:56,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:31:56,342] [INFO] ===== Completeness check finished =====
[2024-01-24 11:31:56,343] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:31:56,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001277175.1_ASM127717v1_genomic.fna/markers.fasta)
[2024-01-24 11:31:56,344] [INFO] Task started: Blastn
[2024-01-24 11:31:56,344] [INFO] Running command: blastn -query GCF_001277175.1_ASM127717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33d2e58a-607e-43e3-bf54-7fe1bf090b06/dqc_reference/reference_markers_gtdb.fasta -out GCF_001277175.1_ASM127717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:57,628] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:57,632] [INFO] Selected 9 target genomes.
[2024-01-24 11:31:57,633] [INFO] Target genome list was writen to GCF_001277175.1_ASM127717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:31:57,640] [INFO] Task started: fastANI
[2024-01-24 11:31:57,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg74228a00-eb1d-4274-b85b-3681ffc5ed5b/GCF_001277175.1_ASM127717v1_genomic.fna.gz --refList GCF_001277175.1_ASM127717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001277175.1_ASM127717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:07,834] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:07,845] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:07,845] [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_001277175.1	s__Cronobacter universalis	100.0	1477	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	conclusive
GCF_001277215.2	s__Cronobacter malonaticus	94.2408	1355	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCA_000027065.2	s__Cronobacter turicensis	94.0813	1359	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_000982825.1	s__Cronobacter sakazakii	93.6786	1324	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
GCF_001277195.1	s__Cronobacter muytjensii	90.113	1295	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_001277235.1	s__Cronobacter dublinensis	90.087	1316	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCF_000026225.1	s__Escherichia fergusonii	80.4947	595	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	98.80	98.39	0.93	0.89	77	-
GCF_005843885.1	s__Escherichia sp005843885	80.4281	645	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	96.83	95.39	0.87	0.80	37	-
GCF_003697165.2	s__Escherichia coli	80.3796	655	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia	95.0	97.07	95.57	0.85	0.72	26859	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:07,847] [INFO] GTDB search result was written to GCF_001277175.1_ASM127717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:07,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:07,851] [INFO] DFAST_QC result json was written to GCF_001277175.1_ASM127717v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:07,851] [INFO] DFAST_QC completed!
[2024-01-24 11:32:07,851] [INFO] Total running time: 0h1m18s