[2024-01-24 10:57:23,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:23,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:23,305] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference
[2024-01-24 10:57:24,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:24,496] [INFO] Task started: Prodigal
[2024-01-24 10:57:24,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg38b3c959-0924-49e5-acfb-591f0f4131ff/GCF_019633665.1_ASM1963366v1_genomic.fna.gz | prodigal -d GCF_019633665.1_ASM1963366v1_genomic.fna/cds.fna -a GCF_019633665.1_ASM1963366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:32,648] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:32,649] [INFO] Task started: HMMsearch
[2024-01-24 10:57:32,649] [INFO] Running command: hmmsearch --tblout GCF_019633665.1_ASM1963366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference/reference_markers.hmm GCF_019633665.1_ASM1963366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:32,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:32,926] [INFO] Found 6/6 markers.
[2024-01-24 10:57:32,951] [INFO] Query marker FASTA was written to GCF_019633665.1_ASM1963366v1_genomic.fna/markers.fasta
[2024-01-24 10:57:32,951] [INFO] Task started: Blastn
[2024-01-24 10:57:32,951] [INFO] Running command: blastn -query GCF_019633665.1_ASM1963366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference/reference_markers.fasta -out GCF_019633665.1_ASM1963366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:33,626] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:33,630] [INFO] Selected 10 target genomes.
[2024-01-24 10:57:33,630] [INFO] Target genome list was writen to GCF_019633665.1_ASM1963366v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:33,634] [INFO] Task started: fastANI
[2024-01-24 10:57:33,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b3c959-0924-49e5-acfb-591f0f4131ff/GCF_019633665.1_ASM1963366v1_genomic.fna.gz --refList GCF_019633665.1_ASM1963366v1_genomic.fna/target_genomes.txt --output GCF_019633665.1_ASM1963366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:41,482] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:41,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:41,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:41,490] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:57:41,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:41,490] [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
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	100.0	934	937	95	conclusive
Pasteurella testudinis	strain=DSM 23072	GCA_900176075.1	761	761	type	True	100.0	934	937	95	conclusive
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	99.9933	935	937	95	conclusive
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	82.3526	606	937	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	82.3422	612	937	95	below_threshold
Spirabiliibacterium mucosae	strain=20609_3	GCA_014884965.1	28156	28156	type	True	77.5402	185	937	95	below_threshold
Citrobacter rodentium	strain=DSM 16636	GCA_021278985.1	67825	67825	type	True	75.7343	70	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:41,491] [INFO] DFAST Taxonomy check result was written to GCF_019633665.1_ASM1963366v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:41,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:41,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:41,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference/checkm_data
[2024-01-24 10:57:41,493] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:41,522] [INFO] Task started: CheckM
[2024-01-24 10:57:41,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019633665.1_ASM1963366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019633665.1_ASM1963366v1_genomic.fna/checkm_input GCF_019633665.1_ASM1963366v1_genomic.fna/checkm_result
[2024-01-24 10:58:10,843] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:10,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:10,861] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:10,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:10,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019633665.1_ASM1963366v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:10,862] [INFO] Task started: Blastn
[2024-01-24 10:58:10,862] [INFO] Running command: blastn -query GCF_019633665.1_ASM1963366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8a24e29-9780-44d3-938a-ee9504a29f6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019633665.1_ASM1963366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:11,782] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:11,785] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:11,785] [INFO] Target genome list was writen to GCF_019633665.1_ASM1963366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:11,806] [INFO] Task started: fastANI
[2024-01-24 10:58:11,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg38b3c959-0924-49e5-acfb-591f0f4131ff/GCF_019633665.1_ASM1963366v1_genomic.fna.gz --refList GCF_019633665.1_ASM1963366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019633665.1_ASM1963366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:19,822] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:19,832] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:19,833] [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_900176075.1	s__Chelonobacter testudinis	100.0	934	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004342725.1	s__Chelonobacter aquarius	82.357	611	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
GCA_006228005.1	s__Chelonobacter sp006228005	82.2785	557	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
GCF_000772535.1	s__Chelonobacter oris	80.5122	561	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014884995.1	s__Spirabiliibacterium pneumoniae	77.9038	149	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014884965.1	s__Spirabiliibacterium mucosae	77.5706	184	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	96.18	96.18	0.92	0.92	2	-
GCA_000752995.2	s__Necropsobacter massiliensis_B	77.4812	180	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004363295.1	s__Mesocricetibacter intestinalis	77.4175	130	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017160915.1	s__Aggregatibacter actinomycetemcomitans_B	77.3033	189	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379785.1	s__Gallibacterium anatis	77.223	96	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	97.46	96.89	0.84	0.80	28	-
GCA_900454475.1	s__Actinobacillus_B mairii	77.1141	113	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438725.1	s__Ewingella americana_A	76.0189	52	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:19,836] [INFO] GTDB search result was written to GCF_019633665.1_ASM1963366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:19,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:19,840] [INFO] DFAST_QC result json was written to GCF_019633665.1_ASM1963366v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:19,840] [INFO] DFAST_QC completed!
[2024-01-24 10:58:19,840] [INFO] Total running time: 0h0m57s