[2024-01-24 13:17:04,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:04,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:04,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference
[2024-01-24 13:17:06,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,042] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,043] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c4edd45-4a4b-453e-8aec-e64098b513cb/GCF_021278985.1_ASM2127898v1_genomic.fna.gz | prodigal -d GCF_021278985.1_ASM2127898v1_genomic.fna/cds.fna -a GCF_021278985.1_ASM2127898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:20,629] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:20,629] [INFO] Task started: HMMsearch
[2024-01-24 13:17:20,629] [INFO] Running command: hmmsearch --tblout GCF_021278985.1_ASM2127898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference/reference_markers.hmm GCF_021278985.1_ASM2127898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:20,945] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:20,946] [INFO] Found 6/6 markers.
[2024-01-24 13:17:20,989] [INFO] Query marker FASTA was written to GCF_021278985.1_ASM2127898v1_genomic.fna/markers.fasta
[2024-01-24 13:17:20,989] [INFO] Task started: Blastn
[2024-01-24 13:17:20,989] [INFO] Running command: blastn -query GCF_021278985.1_ASM2127898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference/reference_markers.fasta -out GCF_021278985.1_ASM2127898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:21,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:21,860] [INFO] Selected 15 target genomes.
[2024-01-24 13:17:21,860] [INFO] Target genome list was writen to GCF_021278985.1_ASM2127898v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:21,864] [INFO] Task started: fastANI
[2024-01-24 13:17:21,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4edd45-4a4b-453e-8aec-e64098b513cb/GCF_021278985.1_ASM2127898v1_genomic.fna.gz --refList GCF_021278985.1_ASM2127898v1_genomic.fna/target_genomes.txt --output GCF_021278985.1_ASM2127898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:38,862] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:38,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:38,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:38,875] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:17:38,875] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:38,875] [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_021278985.1	67825	67825	type	True	100.0	1789	1793	95	conclusive
Citrobacter rodentium	strain=NBRC 105723	GCA_000759815.1	67825	67825	type	True	99.9346	1660	1793	95	conclusive
Citrobacter rodentium	strain=DSM 16636	GCA_015965555.1	67825	67825	type	True	99.9196	1643	1793	95	conclusive
Citrobacter rodentium	strain=ATCC 51116	GCA_015965415.1	67825	67825	type	True	99.9069	1642	1793	95	conclusive
Citrobacter amalonaticus	strain=FDAARGOS_1489	GCA_020099335.1	35703	35703	type	True	85.0095	1168	1793	95	below_threshold
Citrobacter farmeri	strain=FDAARGOS 1423	GCA_019048065.1	67824	67824	type	True	84.9233	1159	1793	95	below_threshold
Citrobacter arsenatis	strain=LY-1	GCA_004353845.1	2546350	2546350	type	True	83.0493	1065	1793	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	82.1982	918	1793	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	82.0764	934	1793	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	82.0607	911	1793	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	81.7734	896	1793	95	below_threshold
Kosakonia sacchari	strain=SP1	GCA_000300455.4	1158459	1158459	type	True	81.1279	875	1793	95	below_threshold
Kosakonia sacchari	strain=CGMCC 1.12102	GCA_900100995.1	1158459	1158459	type	True	81.0243	845	1793	95	below_threshold
Kosakonia quasisacchari	strain=WCHEs120001	GCA_004331415.1	2529380	2529380	type	True	80.8234	800	1793	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:38,877] [INFO] DFAST Taxonomy check result was written to GCF_021278985.1_ASM2127898v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:38,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:38,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:38,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference/checkm_data
[2024-01-24 13:17:38,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:38,930] [INFO] Task started: CheckM
[2024-01-24 13:17:38,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021278985.1_ASM2127898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021278985.1_ASM2127898v1_genomic.fna/checkm_input GCF_021278985.1_ASM2127898v1_genomic.fna/checkm_result
[2024-01-24 13:18:23,562] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:23,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:23,586] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:23,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:23,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021278985.1_ASM2127898v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:23,587] [INFO] Task started: Blastn
[2024-01-24 13:18:23,588] [INFO] Running command: blastn -query GCF_021278985.1_ASM2127898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg836674cd-43ed-4bc6-8133-b9df2950ec20/dqc_reference/reference_markers_gtdb.fasta -out GCF_021278985.1_ASM2127898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:24,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:24,786] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:24,786] [INFO] Target genome list was writen to GCF_021278985.1_ASM2127898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:24,803] [INFO] Task started: fastANI
[2024-01-24 13:18:24,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4edd45-4a4b-453e-8aec-e64098b513cb/GCF_021278985.1_ASM2127898v1_genomic.fna.gz --refList GCF_021278985.1_ASM2127898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021278985.1_ASM2127898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:40,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:40,721] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:40,721] [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	99.9346	1660	1793	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	86.9278	1235	1793	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	85.113	1194	1793	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	85.0153	1188	1793	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	84.9238	1178	1793	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_019048065.1	s__Citrobacter_A farmeri	84.9138	1159	1793	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_018252635.1	s__Citrobacter_A amalonaticus_E	84.7957	1155	1793	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_013836145.1	s__Citrobacter_A sp013836145	84.1857	1112	1793	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	83.5955	1138	1793	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	83.4474	1060	1793	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	83.0669	1062	1793	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	82.7637	1001	1793	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	81.0211	848	1793	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	80.7032	861	1793	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 13:18:40,724] [INFO] GTDB search result was written to GCF_021278985.1_ASM2127898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:40,724] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:40,730] [INFO] DFAST_QC result json was written to GCF_021278985.1_ASM2127898v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:40,730] [INFO] DFAST_QC completed!
[2024-01-24 13:18:40,730] [INFO] Total running time: 0h1m36s