[2024-01-25 17:35:20,370] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:20,372] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:20,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference
[2024-01-25 17:35:21,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:21,618] [INFO] Task started: Prodigal
[2024-01-25 17:35:21,618] [INFO] Running command: gunzip -c /var/lib/cwl/stgd69f0a63-397f-42a8-b052-b1b4bca187d9/GCF_016865525.2_ASM1686552v2_genomic.fna.gz | prodigal -d GCF_016865525.2_ASM1686552v2_genomic.fna/cds.fna -a GCF_016865525.2_ASM1686552v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:39,539] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:39,539] [INFO] Task started: HMMsearch
[2024-01-25 17:35:39,539] [INFO] Running command: hmmsearch --tblout GCF_016865525.2_ASM1686552v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference/reference_markers.hmm GCF_016865525.2_ASM1686552v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:39,838] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:39,839] [INFO] Found 6/6 markers.
[2024-01-25 17:35:39,886] [INFO] Query marker FASTA was written to GCF_016865525.2_ASM1686552v2_genomic.fna/markers.fasta
[2024-01-25 17:35:39,887] [INFO] Task started: Blastn
[2024-01-25 17:35:39,887] [INFO] Running command: blastn -query GCF_016865525.2_ASM1686552v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference/reference_markers.fasta -out GCF_016865525.2_ASM1686552v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:40,708] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:40,711] [INFO] Selected 18 target genomes.
[2024-01-25 17:35:40,712] [INFO] Target genome list was writen to GCF_016865525.2_ASM1686552v2_genomic.fna/target_genomes.txt
[2024-01-25 17:35:40,717] [INFO] Task started: fastANI
[2024-01-25 17:35:40,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgd69f0a63-397f-42a8-b052-b1b4bca187d9/GCF_016865525.2_ASM1686552v2_genomic.fna.gz --refList GCF_016865525.2_ASM1686552v2_genomic.fna/target_genomes.txt --output GCF_016865525.2_ASM1686552v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:00,260] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:00,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:00,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:00,272] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:36:00,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:00,272] [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
Sodalis ligni	strain=dw23	GCA_016865525.2	2697027	2697027	type	True	100.0	2147	2147	95	conclusive
Sodalis ligni	strain=159R	GCA_004346745.1	2697027	2697027	type	True	98.0166	1882	2147	95	conclusive
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	78.44	456	2147	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.4264	485	2147	95	below_threshold
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	78.2317	517	2147	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_002291425.1	929813	929813	type	True	78.1552	452	2147	95	below_threshold
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	78.1502	444	2147	95	below_threshold
Klebsiella quasivariicola	strain=KPN1705	GCA_002269255.1	2026240	2026240	type	True	78.0034	368	2147	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	77.9879	468	2147	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	77.9786	454	2147	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	77.9771	400	2147	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	77.9528	503	2147	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	77.9434	441	2147	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	77.9325	324	2147	95	below_threshold
Enterobacillus tribolii	strain=IG-V01	GCA_019739135.1	1487935	1487935	type	True	77.8383	354	2147	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	77.7624	434	2147	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	77.6393	402	2147	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	77.3875	317	2147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:00,273] [INFO] DFAST Taxonomy check result was written to GCF_016865525.2_ASM1686552v2_genomic.fna/tc_result.tsv
[2024-01-25 17:36:00,274] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:00,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:00,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference/checkm_data
[2024-01-25 17:36:00,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:00,337] [INFO] Task started: CheckM
[2024-01-25 17:36:00,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016865525.2_ASM1686552v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016865525.2_ASM1686552v2_genomic.fna/checkm_input GCF_016865525.2_ASM1686552v2_genomic.fna/checkm_result
[2024-01-25 17:36:51,647] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:51,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:51,669] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:51,669] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:51,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016865525.2_ASM1686552v2_genomic.fna/markers.fasta)
[2024-01-25 17:36:51,671] [INFO] Task started: Blastn
[2024-01-25 17:36:51,671] [INFO] Running command: blastn -query GCF_016865525.2_ASM1686552v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a45a2ef-682d-4405-904e-1ae4694b3019/dqc_reference/reference_markers_gtdb.fasta -out GCF_016865525.2_ASM1686552v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:52,969] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:52,972] [INFO] Selected 9 target genomes.
[2024-01-25 17:36:52,972] [INFO] Target genome list was writen to GCF_016865525.2_ASM1686552v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:52,978] [INFO] Task started: fastANI
[2024-01-25 17:36:52,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgd69f0a63-397f-42a8-b052-b1b4bca187d9/GCF_016865525.2_ASM1686552v2_genomic.fna.gz --refList GCF_016865525.2_ASM1686552v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016865525.2_ASM1686552v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:04,705] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:04,712] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:04,712] [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_016865525.2	s__Acerihabitans sp004346745	100.0	2147	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	98.11	98.11	0.88	0.88	2	conclusive
GCF_018449575.1	s__Acerihabitans sp018449575	88.1544	1585	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010131535.1	s__Acerihabitans arboris	81.201	1004	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654925.1	s__Acerihabitans sp015654925	80.5879	927	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217455.1	s__Acerihabitans sp005217455	79.7713	828	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343195.1	s__Biostraticola tofi	78.8755	490	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Biostraticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517425.1	s__Sodalis_A praecaptivus	78.8687	571	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis_A	96.0224	N/A	N/A	N/A	N/A	1	-
GCF_005484965.1	s__Brenneria nigrifluens	78.4573	459	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Brenneria	95.0	98.35	95.07	0.92	0.76	4	-
GCF_900187015.1	s__Serratia ficaria	78.2997	514	2147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:04,714] [INFO] GTDB search result was written to GCF_016865525.2_ASM1686552v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:04,715] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:04,718] [INFO] DFAST_QC result json was written to GCF_016865525.2_ASM1686552v2_genomic.fna/dqc_result.json
[2024-01-25 17:37:04,718] [INFO] DFAST_QC completed!
[2024-01-25 17:37:04,718] [INFO] Total running time: 0h1m44s