[2024-01-24 11:59:22,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference
[2024-01-24 11:59:25,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,646] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bef6fd4-6b17-46db-b7db-94e5262829db/GCF_016889385.1_ASM1688938v1_genomic.fna.gz | prodigal -d GCF_016889385.1_ASM1688938v1_genomic.fna/cds.fna -a GCF_016889385.1_ASM1688938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:30,644] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:30,644] [INFO] Task started: HMMsearch
[2024-01-24 11:59:30,644] [INFO] Running command: hmmsearch --tblout GCF_016889385.1_ASM1688938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference/reference_markers.hmm GCF_016889385.1_ASM1688938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,893] [INFO] Found 6/6 markers.
[2024-01-24 11:59:30,922] [INFO] Query marker FASTA was written to GCF_016889385.1_ASM1688938v1_genomic.fna/markers.fasta
[2024-01-24 11:59:30,922] [INFO] Task started: Blastn
[2024-01-24 11:59:30,922] [INFO] Running command: blastn -query GCF_016889385.1_ASM1688938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference/reference_markers.fasta -out GCF_016889385.1_ASM1688938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:32,414] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:32,418] [INFO] Selected 7 target genomes.
[2024-01-24 11:59:32,418] [INFO] Target genome list was writen to GCF_016889385.1_ASM1688938v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:32,432] [INFO] Task started: fastANI
[2024-01-24 11:59:32,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bef6fd4-6b17-46db-b7db-94e5262829db/GCF_016889385.1_ASM1688938v1_genomic.fna.gz --refList GCF_016889385.1_ASM1688938v1_genomic.fna/target_genomes.txt --output GCF_016889385.1_ASM1688938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:36,892] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:36,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:36,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:36,902] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:59:36,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:36,902] [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
Haemophilus parahaemolyticus	strain=FDAARGOS_1199	GCA_016889385.1	735	735	type	True	100.0	697	697	95	conclusive
Haemophilus parahaemolyticus	strain=NCTC 8479	GCA_900450675.1	735	735	type	True	99.9998	696	697	95	conclusive
Haemophilus parahaemolyticus	strain=CCUG 3716	GCA_002015035.1	735	735	type	True	99.9796	663	697	95	conclusive
Haemophilus parahaemolyticus	strain=HK385	GCA_000262265.1	735	735	type	True	99.9591	644	697	95	conclusive
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	91.1091	522	697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:36,904] [INFO] DFAST Taxonomy check result was written to GCF_016889385.1_ASM1688938v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:36,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:36,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:36,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference/checkm_data
[2024-01-24 11:59:36,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:36,931] [INFO] Task started: CheckM
[2024-01-24 11:59:36,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016889385.1_ASM1688938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016889385.1_ASM1688938v1_genomic.fna/checkm_input GCF_016889385.1_ASM1688938v1_genomic.fna/checkm_result
[2024-01-24 12:00:01,747] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:01,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:01,761] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:01,762] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:01,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016889385.1_ASM1688938v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:01,763] [INFO] Task started: Blastn
[2024-01-24 12:00:01,763] [INFO] Running command: blastn -query GCF_016889385.1_ASM1688938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2977485c-469b-4b16-a8b2-312904fea6f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016889385.1_ASM1688938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:02,794] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:02,798] [INFO] Selected 12 target genomes.
[2024-01-24 12:00:02,799] [INFO] Target genome list was writen to GCF_016889385.1_ASM1688938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:02,811] [INFO] Task started: fastANI
[2024-01-24 12:00:02,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bef6fd4-6b17-46db-b7db-94e5262829db/GCF_016889385.1_ASM1688938v1_genomic.fna.gz --refList GCF_016889385.1_ASM1688938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016889385.1_ASM1688938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:08,294] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:08,311] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:08,312] [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_002015035.1	s__Haemophilus_A parahaemolyticus	99.9796	663	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.50	95.62	0.95	0.88	11	conclusive
GCA_018373095.1	s__Haemophilus_A parahaemolyticus_A	93.4242	439	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	91.1031	521	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCF_000238795.1	s__Haemophilus_A sputorum	81.0885	285	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	80.1514	292	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_000188255.1	s__Actinobacillus ureae	79.873	248	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	99.22	99.21	0.97	0.96	3	-
GCF_000175195.1	s__Actinobacillus_A minor	79.528	295	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	79.4015	257	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_901687125.1	s__Actinobacillus vicugnae	79.2696	276	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521605.1	s__Mannheimia sp000521605	79.226	258	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	79.0552	251	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377995.1	s__Mannheimia pernigra	78.9683	215	697	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	98.69	97.60	0.91	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:08,314] [INFO] GTDB search result was written to GCF_016889385.1_ASM1688938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:08,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:08,317] [INFO] DFAST_QC result json was written to GCF_016889385.1_ASM1688938v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:08,317] [INFO] DFAST_QC completed!
[2024-01-24 12:00:08,317] [INFO] Total running time: 0h0m45s