[2024-01-24 13:24:48,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,054] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference
[2024-01-24 13:24:49,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,542] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,542] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1b5e82d-4341-4ff0-a682-4858f55bfd18/GCF_000409345.1_Cdlac464_final_contigs_genomic.fna.gz | prodigal -d GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/cds.fna -a GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:01,399] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:01,399] [INFO] Task started: HMMsearch
[2024-01-24 13:25:01,399] [INFO] Running command: hmmsearch --tblout GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference/reference_markers.hmm GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:01,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:01,688] [INFO] Found 6/6 markers.
[2024-01-24 13:25:01,738] [INFO] Query marker FASTA was written to GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/markers.fasta
[2024-01-24 13:25:01,738] [INFO] Task started: Blastn
[2024-01-24 13:25:01,739] [INFO] Running command: blastn -query GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference/reference_markers.fasta -out GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:02,722] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:02,726] [INFO] Selected 11 target genomes.
[2024-01-24 13:25:02,726] [INFO] Target genome list was writen to GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/target_genomes.txt
[2024-01-24 13:25:02,734] [INFO] Task started: fastANI
[2024-01-24 13:25:02,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1b5e82d-4341-4ff0-a682-4858f55bfd18/GCF_000409345.1_Cdlac464_final_contigs_genomic.fna.gz --refList GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/target_genomes.txt --output GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:15,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:15,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:15,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:15,044] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:25:15,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:15,045] [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 dublinensis subsp. lactaridi	strain=LMG 23825	GCA_000409345.1	413499	413497	type	True	100.0	1436	1439	95	conclusive
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	98.2748	1349	1439	95	conclusive
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_001277235.1	413498	413497	type	True	97.4859	1351	1439	95	conclusive
Cronobacter dublinensis subsp. dublinensis	strain=LMG 23823	GCA_000409225.1	413498	413497	type	True	97.4756	1323	1439	95	conclusive
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	92.6326	1254	1439	95	below_threshold
Cronobacter malonaticus	strain=LMG 23826	GCA_000409305.1	413503	413503	type	True	89.8385	1227	1439	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	89.8043	1147	1439	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	81.3303	826	1439	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.265	837	1439	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	81.1844	842	1439	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	81.1576	786	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:15,046] [INFO] DFAST Taxonomy check result was written to GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/tc_result.tsv
[2024-01-24 13:25:15,047] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:15,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:15,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference/checkm_data
[2024-01-24 13:25:15,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:15,092] [INFO] Task started: CheckM
[2024-01-24 13:25:15,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/checkm_input GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/checkm_result
[2024-01-24 13:25:52,286] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:52,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:52,310] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:52,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:52,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/markers.fasta)
[2024-01-24 13:25:52,311] [INFO] Task started: Blastn
[2024-01-24 13:25:52,311] [INFO] Running command: blastn -query GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d6f8ce-fa85-468b-b0f5-8dcd35cf32e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:53,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:53,887] [INFO] Selected 6 target genomes.
[2024-01-24 13:25:53,887] [INFO] Target genome list was writen to GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:53,897] [INFO] Task started: fastANI
[2024-01-24 13:25:53,897] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1b5e82d-4341-4ff0-a682-4858f55bfd18/GCF_000409345.1_Cdlac464_final_contigs_genomic.fna.gz --refList GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/target_genomes_gtdb.txt --output GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:01,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:01,090] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:01,091] [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_001277235.1	s__Cronobacter dublinensis	97.4874	1352	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	conclusive
GCF_001277195.1	s__Cronobacter muytjensii	92.6552	1301	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.13	98.83	0.94	0.91	9	-
GCF_001277175.1	s__Cronobacter universalis	90.4919	1270	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCA_000027065.2	s__Cronobacter turicensis	90.0055	1288	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.17	96.06	0.93	0.89	18	-
GCF_001277215.2	s__Cronobacter malonaticus	89.9163	1278	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.86	98.11	0.94	0.89	62	-
GCF_000982825.1	s__Cronobacter sakazakii	89.8624	1252	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	98.00	97.39	0.92	0.86	440	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,093] [INFO] GTDB search result was written to GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:01,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:01,098] [INFO] DFAST_QC result json was written to GCF_000409345.1_Cdlac464_final_contigs_genomic.fna/dqc_result.json
[2024-01-24 13:26:01,098] [INFO] DFAST_QC completed!
[2024-01-24 13:26:01,099] [INFO] Total running time: 0h1m13s