[2024-01-24 12:09:05,764] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,766] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference
[2024-01-24 12:09:06,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,953] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg366975b4-27fc-4ebc-895b-edd5d583f8c4/GCF_016415625.1_ASM1641562v1_genomic.fna.gz | prodigal -d GCF_016415625.1_ASM1641562v1_genomic.fna/cds.fna -a GCF_016415625.1_ASM1641562v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:17,777] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:17,778] [INFO] Task started: HMMsearch
[2024-01-24 12:09:17,778] [INFO] Running command: hmmsearch --tblout GCF_016415625.1_ASM1641562v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference/reference_markers.hmm GCF_016415625.1_ASM1641562v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:18,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:18,055] [INFO] Found 6/6 markers.
[2024-01-24 12:09:18,088] [INFO] Query marker FASTA was written to GCF_016415625.1_ASM1641562v1_genomic.fna/markers.fasta
[2024-01-24 12:09:18,088] [INFO] Task started: Blastn
[2024-01-24 12:09:18,088] [INFO] Running command: blastn -query GCF_016415625.1_ASM1641562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference/reference_markers.fasta -out GCF_016415625.1_ASM1641562v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:18,923] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:18,927] [INFO] Selected 14 target genomes.
[2024-01-24 12:09:18,928] [INFO] Target genome list was writen to GCF_016415625.1_ASM1641562v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:18,933] [INFO] Task started: fastANI
[2024-01-24 12:09:18,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg366975b4-27fc-4ebc-895b-edd5d583f8c4/GCF_016415625.1_ASM1641562v1_genomic.fna.gz --refList GCF_016415625.1_ASM1641562v1_genomic.fna/target_genomes.txt --output GCF_016415625.1_ASM1641562v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:09:31,690] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:31,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:09:31,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:09:31,706] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:09:31,706] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:09:31,707] [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
Shimwellia pseudoproteus	strain=DSM 3038	GCA_016415625.1	570012	570012	type	True	100.0	1322	1329	95	conclusive
Shimwellia blattae	strain=DSM 4481	GCA_000262305.1	563	563	type	True	84.5632	971	1329	95	below_threshold
Shimwellia blattae	strain=NCTC12127	GCA_900636035.1	563	563	type	True	84.5538	975	1329	95	below_threshold
Shimwellia blattae	strain=NBRC 105725	GCA_000327265.1	563	563	type	True	84.4618	956	1329	95	below_threshold
Atlantibacter hermannii	strain=FDAARGOS_888	GCA_016027855.1	565	565	type	True	79.838	488	1329	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	79.7924	573	1329	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.7149	542	1329	95	below_threshold
Enterobacter hormaechei subsp. steigerwaltii	strain=DSM 16691	GCA_001729725.1	299766	158836	type	True	79.687	547	1329	95	below_threshold
Cronobacter dublinensis subsp. lausannensis	strain=LMG 23824	GCA_000409365.1	413500	413497	type	True	79.5923	532	1329	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	79.5855	550	1329	95	below_threshold
Klebsiella pneumoniae subsp. pneumoniae	strain=ATCC 13883	GCA_000788015.1	72407	573	type	True	79.5399	637	1329	95	below_threshold
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	79.4956	630	1329	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	79.4868	510	1329	95	below_threshold
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	79.278	482	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:09:31,709] [INFO] DFAST Taxonomy check result was written to GCF_016415625.1_ASM1641562v1_genomic.fna/tc_result.tsv
[2024-01-24 12:09:31,709] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:09:31,709] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:09:31,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference/checkm_data
[2024-01-24 12:09:31,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:09:31,749] [INFO] Task started: CheckM
[2024-01-24 12:09:31,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016415625.1_ASM1641562v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016415625.1_ASM1641562v1_genomic.fna/checkm_input GCF_016415625.1_ASM1641562v1_genomic.fna/checkm_result
[2024-01-24 12:10:06,789] [INFO] Task succeeded: CheckM
[2024-01-24 12:10:06,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:10:06,813] [INFO] ===== Completeness check finished =====
[2024-01-24 12:10:06,814] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:10:06,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016415625.1_ASM1641562v1_genomic.fna/markers.fasta)
[2024-01-24 12:10:06,815] [INFO] Task started: Blastn
[2024-01-24 12:10:06,815] [INFO] Running command: blastn -query GCF_016415625.1_ASM1641562v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9f70f76-344f-4cb9-85e0-af582a6c9fd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016415625.1_ASM1641562v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:10:07,927] [INFO] Task succeeded: Blastn
[2024-01-24 12:10:07,930] [INFO] Selected 24 target genomes.
[2024-01-24 12:10:07,931] [INFO] Target genome list was writen to GCF_016415625.1_ASM1641562v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:10:07,946] [INFO] Task started: fastANI
[2024-01-24 12:10:07,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg366975b4-27fc-4ebc-895b-edd5d583f8c4/GCF_016415625.1_ASM1641562v1_genomic.fna.gz --refList GCF_016415625.1_ASM1641562v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016415625.1_ASM1641562v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:28,579] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:28,597] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:28,598] [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_016415625.1	s__Shimwellia pseudoproteus	100.0	1322	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000262305.1	s__Shimwellia blattae	84.5569	970	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Shimwellia	95.0	99.99	99.99	1.00	1.00	4	-
GCF_009907385.1	s__Atlantibacter hermannii_A	79.9321	541	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570865.1	s__Atlantibacter subterranea	79.8644	574	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.55	98.44	0.93	0.91	8	-
GCF_000164865.1	s__Enterobacter_B lignolyticus	79.8233	598	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter_B	95.0	98.80	98.80	0.94	0.94	2	-
GCF_014193285.1	s__Atlantibacter sp002345315	79.7092	576	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_011754535.1	s__Enterobacter cloacae_N	79.6954	553	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_001277235.1	s__Cronobacter dublinensis	79.6745	539	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	97.74	96.92	0.93	0.89	42	-
GCA_900635495.1	s__Atlantibacter hermannii	79.6481	503	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.95	98.59	0.96	0.90	28	-
GCF_002208095.1	s__Enterobacter cloacae_M	79.6452	579	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
GCF_001277175.1	s__Cronobacter universalis	79.6439	552	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cronobacter	95.0	99.87	99.62	0.99	0.98	4	-
GCF_009755685.1	s__Enterobacter sp000568095	79.6332	573	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCA_001484765.1	s__Erwinia_A teleogrylli	79.6153	631	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000463155.2	s__Siccibacter turicensis	79.5971	539	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Siccibacter	95.0	98.74	97.87	0.95	0.92	6	-
GCF_015234305.1	s__Superficieibacter sp900766525	79.5405	525	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Superficieibacter	95.0	96.26	96.26	0.86	0.86	2	-
GCF_000742135.1	s__Klebsiella pneumoniae	79.4422	632	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	98.97	95.97	0.88	0.77	11294	-
GCF_900978845.1	s__Klebsiella africana	79.3653	609	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_016756775.1	s__Buttiauxella davisae_A	79.2936	530	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003818135.1	s__Buttiauxella warmboldiae	79.2874	481	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003601925.1	s__Buttiauxella izardii	79.0386	481	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220655.1	s__Serratia marcescens_K	78.5359	429	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.0833	98.79	98.10	0.94	0.88	411	-
--------------------------------------------------------------------------------
[2024-01-24 12:10:28,599] [INFO] GTDB search result was written to GCF_016415625.1_ASM1641562v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:28,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:28,603] [INFO] DFAST_QC result json was written to GCF_016415625.1_ASM1641562v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:28,603] [INFO] DFAST_QC completed!
[2024-01-24 12:10:28,604] [INFO] Total running time: 0h1m23s