[2024-01-24 15:06:36,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference
[2024-01-24 15:06:38,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,142] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,142] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf3a9ccb-cbb5-4eba-9bed-e15ef96c559a/GCF_004346745.1_ASM434674v1_genomic.fna.gz | prodigal -d GCF_004346745.1_ASM434674v1_genomic.fna/cds.fna -a GCF_004346745.1_ASM434674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:56,773] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:56,774] [INFO] Task started: HMMsearch
[2024-01-24 15:06:56,774] [INFO] Running command: hmmsearch --tblout GCF_004346745.1_ASM434674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference/reference_markers.hmm GCF_004346745.1_ASM434674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:57,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:57,144] [INFO] Found 6/6 markers.
[2024-01-24 15:06:57,197] [INFO] Query marker FASTA was written to GCF_004346745.1_ASM434674v1_genomic.fna/markers.fasta
[2024-01-24 15:06:57,197] [INFO] Task started: Blastn
[2024-01-24 15:06:57,197] [INFO] Running command: blastn -query GCF_004346745.1_ASM434674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference/reference_markers.fasta -out GCF_004346745.1_ASM434674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:58,106] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:58,109] [INFO] Selected 18 target genomes.
[2024-01-24 15:06:58,110] [INFO] Target genome list was writen to GCF_004346745.1_ASM434674v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:58,118] [INFO] Task started: fastANI
[2024-01-24 15:06:58,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf3a9ccb-cbb5-4eba-9bed-e15ef96c559a/GCF_004346745.1_ASM434674v1_genomic.fna.gz --refList GCF_004346745.1_ASM434674v1_genomic.fna/target_genomes.txt --output GCF_004346745.1_ASM434674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:16,783] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:16,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:16,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:16,798] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:07:16,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:16,799] [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=159R	GCA_004346745.1	2697027	2697027	type	True	100.0	2128	2128	95	conclusive
Sodalis ligni	strain=dw23	GCA_016865525.2	2697027	2697027	type	True	98.1149	1871	2128	95	conclusive
Serratia ficaria	strain=NCTC12148	GCA_900187015.1	61651	61651	type	True	78.6878	509	2128	95	below_threshold
Brenneria nigrifluens	strain=ATCC 13028	GCA_005484965.1	55210	55210	type	True	78.5779	436	2128	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.5668	482	2128	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	78.4807	447	2128	95	below_threshold
Brenneria nigrifluens	strain=LMG 2694	GCA_003115835.1	55210	55210	type	True	78.3546	427	2128	95	below_threshold
Serratia ficaria	strain=NBRC 102596	GCA_001590885.1	61651	61651	type	True	78.2346	495	2128	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_002291425.1	929813	929813	type	True	78.2216	445	2128	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.1237	473	2128	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_001644705.1	1089444	1089444	type	True	78.0171	414	2128	95	below_threshold
Gibbsiella quercinecans	strain=FRB97	GCA_003666185.1	929813	929813	type	True	77.9778	432	2128	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	77.9077	459	2128	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	77.889	330	2128	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	77.8222	414	2128	95	below_threshold
Enterobacillus tribolii	strain=IG-V01	GCA_019739135.1	1487935	1487935	type	True	77.7713	363	2128	95	below_threshold
Dickeya solani	strain=IPO 2222	GCA_000400795.1	1089444	1089444	type	True	77.6736	407	2128	95	below_threshold
Musicola keenii	strain=A3967	GCA_022761095.1	2884250	2884250	type	True	77.5041	317	2128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:16,801] [INFO] DFAST Taxonomy check result was written to GCF_004346745.1_ASM434674v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:16,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:16,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:16,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference/checkm_data
[2024-01-24 15:07:16,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:16,880] [INFO] Task started: CheckM
[2024-01-24 15:07:16,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346745.1_ASM434674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346745.1_ASM434674v1_genomic.fna/checkm_input GCF_004346745.1_ASM434674v1_genomic.fna/checkm_result
[2024-01-24 15:08:08,907] [INFO] Task succeeded: CheckM
[2024-01-24 15:08:08,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:08:08,930] [INFO] ===== Completeness check finished =====
[2024-01-24 15:08:08,931] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:08:08,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346745.1_ASM434674v1_genomic.fna/markers.fasta)
[2024-01-24 15:08:08,932] [INFO] Task started: Blastn
[2024-01-24 15:08:08,932] [INFO] Running command: blastn -query GCF_004346745.1_ASM434674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29552727-e799-4f8c-b67b-a06bf332cea6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346745.1_ASM434674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:08:10,256] [INFO] Task succeeded: Blastn
[2024-01-24 15:08:10,260] [INFO] Selected 10 target genomes.
[2024-01-24 15:08:10,261] [INFO] Target genome list was writen to GCF_004346745.1_ASM434674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:08:10,279] [INFO] Task started: fastANI
[2024-01-24 15:08:10,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf3a9ccb-cbb5-4eba-9bed-e15ef96c559a/GCF_004346745.1_ASM434674v1_genomic.fna.gz --refList GCF_004346745.1_ASM434674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346745.1_ASM434674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:22,416] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:22,430] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:22,430] [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	98.1149	1871	2128	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	88.2268	1549	2128	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	81.1481	1005	2128	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	80.6438	941	2128	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	79.6915	839	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Acerihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143145.1	s__SoCistrobi sp900143145	79.2638	381	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__SoCistrobi	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517425.1	s__Sodalis_A praecaptivus	79.226	557	2128	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_004343195.1	s__Biostraticola tofi	78.9192	490	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Biostraticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187015.1	s__Serratia ficaria	78.5929	506	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCF_016742975.1	s__Serratia nevei	78.2401	412	2128	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.1913	97.82	96.26	0.83	0.75	139	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:22,432] [INFO] GTDB search result was written to GCF_004346745.1_ASM434674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:22,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:22,436] [INFO] DFAST_QC result json was written to GCF_004346745.1_ASM434674v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:22,436] [INFO] DFAST_QC completed!
[2024-01-24 15:08:22,436] [INFO] Total running time: 0h1m46s