[2024-01-24 13:17:34,159] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,161] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,162] [INFO] DQC Reference Directory: /var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference
[2024-01-24 13:17:35,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,732] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg88a1f7d3-9da5-4a41-a3ff-1ef7054e0c1a/GCF_025215095.1_ASM2521509v1_genomic.fna.gz | prodigal -d GCF_025215095.1_ASM2521509v1_genomic.fna/cds.fna -a GCF_025215095.1_ASM2521509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:48,024] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:48,025] [INFO] Task started: HMMsearch
[2024-01-24 13:17:48,025] [INFO] Running command: hmmsearch --tblout GCF_025215095.1_ASM2521509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference/reference_markers.hmm GCF_025215095.1_ASM2521509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:48,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:48,337] [INFO] Found 6/6 markers.
[2024-01-24 13:17:48,380] [INFO] Query marker FASTA was written to GCF_025215095.1_ASM2521509v1_genomic.fna/markers.fasta
[2024-01-24 13:17:48,380] [INFO] Task started: Blastn
[2024-01-24 13:17:48,380] [INFO] Running command: blastn -query GCF_025215095.1_ASM2521509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference/reference_markers.fasta -out GCF_025215095.1_ASM2521509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:49,321] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:49,324] [INFO] Selected 17 target genomes.
[2024-01-24 13:17:49,324] [INFO] Target genome list was writen to GCF_025215095.1_ASM2521509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:49,330] [INFO] Task started: fastANI
[2024-01-24 13:17:49,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a1f7d3-9da5-4a41-a3ff-1ef7054e0c1a/GCF_025215095.1_ASM2521509v1_genomic.fna.gz --refList GCF_025215095.1_ASM2521509v1_genomic.fna/target_genomes.txt --output GCF_025215095.1_ASM2521509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:06,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:06,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:06,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:06,966] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:06,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:06,966] [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
Buttiauxella warmboldiae	strain=CCUG 35512	GCA_003818135.1	82993	82993	type	True	82.863	811	1449	95	below_threshold
Buttiauxella izardii	strain=CCUG 35510	GCA_003601925.1	82991	82991	type	True	82.5657	953	1449	95	below_threshold
Buttiauxella agrestis	strain=NCTC12119	GCA_900446255.1	82977	82977	type	True	82.3575	957	1449	95	below_threshold
Buttiauxella brennerae	strain=ATCC 51605	GCA_001654925.1	82988	82988	type	True	82.3421	906	1449	95	below_threshold
Buttiauxella agrestis	strain=ATCC 33320	GCA_000735355.1	82977	82977	type	True	82.3129	931	1449	95	below_threshold
Buttiauxella gaviniae	strain=ATCC 51604	GCA_001654835.1	82990	82990	type	True	82.2736	919	1449	95	below_threshold
Buttiauxella massiliensis	strain=Marseille-P9829	GCA_902500225.1	2831590	2831590	type	True	82.2378	904	1449	95	below_threshold
Buttiauxella ferragutiae	strain=ATCC 51602	GCA_001654915.1	82989	82989	type	True	82.215	894	1449	95	below_threshold
Cedecea davisae	strain=NCTC13724	GCA_900446735.1	158484	158484	type	True	81.9708	876	1449	95	below_threshold
Cedecea davisae	strain=DSM 4568	GCA_000412335.2	158484	158484	type	True	81.857	880	1449	95	below_threshold
Cedecea neteri	strain=NBRC 105707	GCA_001571265.1	158822	158822	suspected-type	True	81.7438	805	1449	95	below_threshold
Cedecea lapagei	strain=NCTC11466	GCA_900635955.1	158823	158823	type	True	81.6274	831	1449	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	80.4482	727	1449	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	80.1874	712	1449	95	below_threshold
Pseudocitrobacter corydidari		GCA_021172065.1	2891570	2891570	type	True	80.0496	712	1449	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	80.0273	717	1449	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	80.0015	711	1449	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:06,968] [INFO] DFAST Taxonomy check result was written to GCF_025215095.1_ASM2521509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:06,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:06,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:06,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference/checkm_data
[2024-01-24 13:18:06,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:07,016] [INFO] Task started: CheckM
[2024-01-24 13:18:07,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025215095.1_ASM2521509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025215095.1_ASM2521509v1_genomic.fna/checkm_input GCF_025215095.1_ASM2521509v1_genomic.fna/checkm_result
[2024-01-24 13:18:47,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:47,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:47,559] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:47,560] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:47,560] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025215095.1_ASM2521509v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:47,560] [INFO] Task started: Blastn
[2024-01-24 13:18:47,561] [INFO] Running command: blastn -query GCF_025215095.1_ASM2521509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg622508d5-e90e-43c2-a4e0-e931c8980f51/dqc_reference/reference_markers_gtdb.fasta -out GCF_025215095.1_ASM2521509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:49,012] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:49,016] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:49,016] [INFO] Target genome list was writen to GCF_025215095.1_ASM2521509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:49,043] [INFO] Task started: fastANI
[2024-01-24 13:18:49,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a1f7d3-9da5-4a41-a3ff-1ef7054e0c1a/GCF_025215095.1_ASM2521509v1_genomic.fna.gz --refList GCF_025215095.1_ASM2521509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025215095.1_ASM2521509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:04,052] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:04,070] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:04,070] [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_003628475.1	s__Buttiauxella sp002321695	88.5466	1180	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	99.11	99.11	0.94	0.94	2	-
GCF_011808225.1	s__Buttiauxella colo	88.5015	1135	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756775.1	s__Buttiauxella davisae_A	84.2668	1004	1449	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	82.8623	812	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654925.1	s__Buttiauxella brennerae	82.3273	908	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735355.1	s__Buttiauxella agrestis	82.3008	933	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	96.92	96.37	0.91	0.90	3	-
GCF_001654915.1	s__Buttiauxella ferragutiae	82.2149	894	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	99.06	98.93	0.93	0.91	3	-
GCF_006376615.1	s__Buttiauxella sp006376615	81.891	868	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412335.2	s__Cedecea davisae	81.8685	878	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	98.19	96.20	0.94	0.89	6	-
GCF_001571265.1	s__Cedecea neteri	81.7464	805	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	99.91	99.83	0.99	0.99	3	-
GCF_000758325.1	s__Cedecea neteri_B	81.6043	838	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752815.1	s__Cedecea sp011752815	81.5948	822	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758305.1	s__Cedecea neteri_C	81.5592	837	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	97.60	97.60	0.88	0.88	2	-
GCA_009668225.1	s__Cedecea sp009668225	81.53	840	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963575.1	s__Cedecea michiganensis_A	81.5077	836	1449	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Cedecea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:04,072] [INFO] GTDB search result was written to GCF_025215095.1_ASM2521509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:04,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:04,078] [INFO] DFAST_QC result json was written to GCF_025215095.1_ASM2521509v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:04,078] [INFO] DFAST_QC completed!
[2024-01-24 13:19:04,078] [INFO] Total running time: 0h1m30s