[2023-06-16 21:16:45,080] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:16:45,082] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:16:45,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference
[2023-06-16 21:16:47,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:16:47,531] [INFO] Task started: Prodigal
[2023-06-16 21:16:47,531] [INFO] Running command: gunzip -c /var/lib/cwl/stga682076c-3c31-4cb9-a4bd-3eeb7ec8bf39/GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna.gz | prodigal -d GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/cds.fna -a GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:17:01,346] [INFO] Task succeeded: Prodigal
[2023-06-16 21:17:01,346] [INFO] Task started: HMMsearch
[2023-06-16 21:17:01,346] [INFO] Running command: hmmsearch --tblout GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference/reference_markers.hmm GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:17:01,665] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:17:01,666] [INFO] Found 6/6 markers.
[2023-06-16 21:17:01,725] [INFO] Query marker FASTA was written to GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/markers.fasta
[2023-06-16 21:17:01,725] [INFO] Task started: Blastn
[2023-06-16 21:17:01,726] [INFO] Running command: blastn -query GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/markers.fasta -db /var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference/reference_markers.fasta -out GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:17:02,673] [INFO] Task succeeded: Blastn
[2023-06-16 21:17:02,677] [INFO] Selected 10 target genomes.
[2023-06-16 21:17:02,677] [INFO] Target genome list was writen to GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/target_genomes.txt
[2023-06-16 21:17:02,680] [INFO] Task started: fastANI
[2023-06-16 21:17:02,680] [INFO] Running command: fastANI --query /var/lib/cwl/stga682076c-3c31-4cb9-a4bd-3eeb7ec8bf39/GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna.gz --refList GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/target_genomes.txt --output GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:17:14,938] [INFO] Task succeeded: fastANI
[2023-06-16 21:17:14,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:17:14,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:17:14,948] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-06-16 21:17:14,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-16 21:17:14,949] [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
Klebsiella variicola	strain=F2R9	GCA_017638945.1	244366	244366	type	True	98.9228	1655	1773	95	conclusive
Klebsiella variicola subsp. variicola	strain=F2R9T	GCA_020525545.1	2590157	244366	type	True	98.9182	1655	1773	95	conclusive
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	98.916	1656	1773	95	conclusive
Klebsiella variicola	strain=DSM 15968	GCA_020115545.1	244366	244366	type	True	98.8994	1644	1773	95	conclusive
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	98.8917	1631	1773	95	conclusive
Klebsiella pneumoniae	strain=PartO-Kpneumoniae-RM8376	GCA_022869665.1	573	573	type	True	94.6141	1521	1773	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.0925	898	1773	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	81.7499	936	1773	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.7238	912	1773	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	81.6107	903	1773	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:17:14,951] [INFO] DFAST Taxonomy check result was written to GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/tc_result.tsv
[2023-06-16 21:17:14,951] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:17:14,951] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:17:14,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference/checkm_data
[2023-06-16 21:17:14,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:17:15,004] [INFO] Task started: CheckM
[2023-06-16 21:17:15,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/checkm_input GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/checkm_result
[2023-06-16 21:17:57,721] [INFO] Task succeeded: CheckM
[2023-06-16 21:17:57,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:17:57,742] [INFO] ===== Completeness check finished =====
[2023-06-16 21:17:57,742] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:17:57,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/markers.fasta)
[2023-06-16 21:17:57,743] [INFO] Task started: Blastn
[2023-06-16 21:17:57,743] [INFO] Running command: blastn -query GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/markers.fasta -db /var/lib/cwl/stg1230e426-6bef-455b-8696-97af62a5b55a/dqc_reference/reference_markers_gtdb.fasta -out GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:17:59,001] [INFO] Task succeeded: Blastn
[2023-06-16 21:17:59,005] [INFO] Selected 10 target genomes.
[2023-06-16 21:17:59,006] [INFO] Target genome list was writen to GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:17:59,010] [INFO] Task started: fastANI
[2023-06-16 21:17:59,011] [INFO] Running command: fastANI --query /var/lib/cwl/stga682076c-3c31-4cb9-a4bd-3eeb7ec8bf39/GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna.gz --refList GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/target_genomes_gtdb.txt --output GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:18:11,393] [INFO] Task succeeded: fastANI
[2023-06-16 21:18:11,402] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:18:11,403] [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_000828055.2	s__Klebsiella variicola	98.916	1656	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.94	96.87	0.93	0.84	528	conclusive
GCF_000742135.1	s__Klebsiella pneumoniae	94.6347	1505	1773	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	94.2493	1538	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.216	95.65	95.27	0.93	0.90	27	-
GCF_000751755.1	s__Klebsiella quasipneumoniae	93.5452	1531	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	97.20	95.71	0.90	0.83	644	-
GCF_000215745.1	s__Klebsiella aerogenes	86.2008	1205	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	98.40	95.78	0.92	0.85	341	-
GCF_004342285.1	s__Klebsiella sp004342285	84.0448	1220	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735435.1	s__Klebsiella planticola	83.794	1240	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella	95.7194	99.21	98.49	0.93	0.89	44	-
GCA_002211745.1	s__Kluyvera georgiana_A	82.1642	939	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kluyvera	95.0	98.12	98.12	0.89	0.89	2	-
GCF_013375935.1	s__Enterobacter cloacae_O	81.6698	928	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_000016325.1	s__Lelliottia sp000016325	80.7715	789	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	95.60	95.60	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-16 21:18:11,405] [INFO] GTDB search result was written to GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/result_gtdb.tsv
[2023-06-16 21:18:11,405] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:18:11,409] [INFO] DFAST_QC result json was written to GCA_905200345.1_ERR1600669-mag-bin.34_genomic.fna/dqc_result.json
[2023-06-16 21:18:11,409] [INFO] DFAST_QC completed!
[2023-06-16 21:18:11,409] [INFO] Total running time: 0h1m26s