[2024-01-24 11:12:36,734] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference
[2024-01-24 11:12:38,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,015] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4dfa645-bc67-4c0a-8e7d-b05bc9b01114/GCF_015965555.1_PDT000619840.1_genomic.fna.gz | prodigal -d GCF_015965555.1_PDT000619840.1_genomic.fna/cds.fna -a GCF_015965555.1_PDT000619840.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,831] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,831] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,832] [INFO] Running command: hmmsearch --tblout GCF_015965555.1_PDT000619840.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference/reference_markers.hmm GCF_015965555.1_PDT000619840.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:51,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:51,141] [INFO] Found 6/6 markers.
[2024-01-24 11:12:51,188] [INFO] Query marker FASTA was written to GCF_015965555.1_PDT000619840.1_genomic.fna/markers.fasta
[2024-01-24 11:12:51,188] [INFO] Task started: Blastn
[2024-01-24 11:12:51,189] [INFO] Running command: blastn -query GCF_015965555.1_PDT000619840.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference/reference_markers.fasta -out GCF_015965555.1_PDT000619840.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:52,050] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:52,053] [INFO] Selected 15 target genomes.
[2024-01-24 11:12:52,054] [INFO] Target genome list was writen to GCF_015965555.1_PDT000619840.1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:52,059] [INFO] Task started: fastANI
[2024-01-24 11:12:52,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4dfa645-bc67-4c0a-8e7d-b05bc9b01114/GCF_015965555.1_PDT000619840.1_genomic.fna.gz --refList GCF_015965555.1_PDT000619840.1_genomic.fna/target_genomes.txt --output GCF_015965555.1_PDT000619840.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:08,304] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:08,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:08,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:08,317] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:13:08,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:08,318] [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
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	100.0	1643	1664	95	conclusive
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	99.9989	1642	1664	95	conclusive
Citrobacter rodentium	strain=NBRC 105723	GCA_000759815.1	67825	67825	type	True	99.9912	1634	1664	95	conclusive
Citrobacter rodentium	strain=ATCC 51116	GCA_015965415.1	67825	67825	type	True	99.9887	1633	1664	95	conclusive
Citrobacter amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	84.9392	1123	1664	95	below_threshold
Citrobacter farmeri	strain=FDAARGOS 1423	GCA_019048065.1	67824	67824	type	True	84.686	1140	1664	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	83.0106	1017	1664	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.2453	881	1664	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.1871	872	1664	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	82.1439	879	1664	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.9645	847	1664	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	81.1594	800	1664	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	81.1419	797	1664	95	below_threshold
Kosakonia quasisacchari	strain=WCHEs120001	GCA_004331415.1	2529380	2529380	type	True	80.8473	774	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,319] [INFO] DFAST Taxonomy check result was written to GCF_015965555.1_PDT000619840.1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:08,320] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:08,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:08,321] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference/checkm_data
[2024-01-24 11:13:08,322] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:08,379] [INFO] Task started: CheckM
[2024-01-24 11:13:08,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015965555.1_PDT000619840.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015965555.1_PDT000619840.1_genomic.fna/checkm_input GCF_015965555.1_PDT000619840.1_genomic.fna/checkm_result
[2024-01-24 11:13:49,285] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:49,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:49,309] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:49,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:49,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015965555.1_PDT000619840.1_genomic.fna/markers.fasta)
[2024-01-24 11:13:49,310] [INFO] Task started: Blastn
[2024-01-24 11:13:49,311] [INFO] Running command: blastn -query GCF_015965555.1_PDT000619840.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60948139-a404-4185-a3b5-62230a9685b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_015965555.1_PDT000619840.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:50,592] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:50,597] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:50,598] [INFO] Target genome list was writen to GCF_015965555.1_PDT000619840.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:50,609] [INFO] Task started: fastANI
[2024-01-24 11:13:50,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4dfa645-bc67-4c0a-8e7d-b05bc9b01114/GCF_015965555.1_PDT000619840.1_genomic.fna.gz --refList GCF_015965555.1_PDT000619840.1_genomic.fna/target_genomes_gtdb.txt --output GCF_015965555.1_PDT000619840.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:06,216] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:06,232] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:06,232] [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_000759815.1	s__Citrobacter_A rodentium	99.9912	1634	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.98	99.96	0.98	0.96	4	conclusive
GCF_000759835.1	s__Citrobacter_A sedlakii	86.8817	1225	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.16	99.00	0.95	0.93	10	-
GCF_000981805.1	s__Citrobacter_A amalonaticus_C	85.0991	1138	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363175.1	s__Citrobacter_A telavivensis	85.0009	1148	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018323885.1	s__Citrobacter_A amalonaticus	84.9674	1122	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.67	95.02	0.91	0.83	59	-
GCF_018252635.1	s__Citrobacter_A amalonaticus_E	84.8114	1120	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019048065.1	s__Citrobacter_A farmeri	84.6879	1140	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	98.22	96.70	0.93	0.90	16	-
GCF_013836145.1	s__Citrobacter_A sp013836145	84.049	1071	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002918555.1	s__Citrobacter_C amalonaticus_A	83.7424	1088	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter_C	95.0	100.00	100.00	1.00	1.00	4	-
GCF_000155975.1	s__Citrobacter portucalensis_A	83.4207	1040	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004353845.1	s__Citrobacter freundii_E	83.0112	1018	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	99.27	99.27	0.92	0.92	2	-
GCF_005281345.1	s__Citrobacter sp005281345	82.8346	963	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	97.53	97.53	0.86	0.86	2	-
GCF_014193285.1	s__Atlantibacter sp002345315	80.9477	832	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Atlantibacter	95.0	98.54	98.53	0.93	0.90	4	-
GCF_902706235.1	s__Scandinavium sp902706235	80.8164	821	1664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:06,234] [INFO] GTDB search result was written to GCF_015965555.1_PDT000619840.1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:06,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:06,238] [INFO] DFAST_QC result json was written to GCF_015965555.1_PDT000619840.1_genomic.fna/dqc_result.json
[2024-01-24 11:14:06,238] [INFO] DFAST_QC completed!
[2024-01-24 11:14:06,238] [INFO] Total running time: 0h1m30s