[2024-01-25 19:45:05,372] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:05,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:05,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference
[2024-01-25 19:45:06,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:06,454] [INFO] Task started: Prodigal
[2024-01-25 19:45:06,454] [INFO] Running command: gunzip -c /var/lib/cwl/stgffda7542-055a-4e50-847d-59de3e4fa25f/GCF_900450845.1_45473_E02_genomic.fna.gz | prodigal -d GCF_900450845.1_45473_E02_genomic.fna/cds.fna -a GCF_900450845.1_45473_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:10,697] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:10,697] [INFO] Task started: HMMsearch
[2024-01-25 19:45:10,697] [INFO] Running command: hmmsearch --tblout GCF_900450845.1_45473_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference/reference_markers.hmm GCF_900450845.1_45473_E02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:10,906] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:10,907] [INFO] Found 6/6 markers.
[2024-01-25 19:45:10,930] [INFO] Query marker FASTA was written to GCF_900450845.1_45473_E02_genomic.fna/markers.fasta
[2024-01-25 19:45:10,930] [INFO] Task started: Blastn
[2024-01-25 19:45:10,930] [INFO] Running command: blastn -query GCF_900450845.1_45473_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference/reference_markers.fasta -out GCF_900450845.1_45473_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:11,603] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:11,605] [INFO] Selected 12 target genomes.
[2024-01-25 19:45:11,606] [INFO] Target genome list was writen to GCF_900450845.1_45473_E02_genomic.fna/target_genomes.txt
[2024-01-25 19:45:11,615] [INFO] Task started: fastANI
[2024-01-25 19:45:11,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgffda7542-055a-4e50-847d-59de3e4fa25f/GCF_900450845.1_45473_E02_genomic.fna.gz --refList GCF_900450845.1_45473_E02_genomic.fna/target_genomes.txt --output GCF_900450845.1_45473_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:18,641] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:18,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:18,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:18,650] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:45:18,650] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:18,651] [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 parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	100.0	715	715	95	conclusive
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	99.9973	711	715	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	99.9768	699	715	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	99.9454	703	715	95	conclusive
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	83.2601	359	715	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	81.15	335	715	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.5923	318	715	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	79.3666	55	715	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	79.144	59	715	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	78.9849	286	715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:18,652] [INFO] DFAST Taxonomy check result was written to GCF_900450845.1_45473_E02_genomic.fna/tc_result.tsv
[2024-01-25 19:45:18,652] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:18,652] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:18,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference/checkm_data
[2024-01-25 19:45:18,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:18,689] [INFO] Task started: CheckM
[2024-01-25 19:45:18,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900450845.1_45473_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900450845.1_45473_E02_genomic.fna/checkm_input GCF_900450845.1_45473_E02_genomic.fna/checkm_result
[2024-01-25 19:45:37,202] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:37,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:37,217] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:37,217] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:37,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900450845.1_45473_E02_genomic.fna/markers.fasta)
[2024-01-25 19:45:37,217] [INFO] Task started: Blastn
[2024-01-25 19:45:37,218] [INFO] Running command: blastn -query GCF_900450845.1_45473_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stg4783050c-20fa-45cf-9ab3-a0c06dd6e252/dqc_reference/reference_markers_gtdb.fasta -out GCF_900450845.1_45473_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:38,374] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:38,377] [INFO] Selected 15 target genomes.
[2024-01-25 19:45:38,377] [INFO] Target genome list was writen to GCF_900450845.1_45473_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:38,391] [INFO] Task started: fastANI
[2024-01-25 19:45:38,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgffda7542-055a-4e50-847d-59de3e4fa25f/GCF_900450845.1_45473_E02_genomic.fna.gz --refList GCF_900450845.1_45473_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900450845.1_45473_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:44,982] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:44,992] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:44,992] [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_000191405.1	s__Haemophilus_D parainfluenzae	99.9454	703	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	conclusive
GCF_003252755.1	s__Haemophilus_D parainfluenzae_N	94.5876	600	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.46	95.02	0.94	0.93	5	-
GCA_905214375.1	s__Haemophilus_D sp905214375	94.5744	494	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCF_014931395.1	s__Haemophilus_D sp900764435	94.4023	609	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.55	95.23	0.94	0.91	6	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	94.2666	581	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	94.0564	601	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCF_001815355.1	s__Haemophilus_D sp001815355	93.994	569	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.35	95.20	0.94	0.91	8	-
GCA_900756155.1	s__Haemophilus_D sp900756155	93.8882	568	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCA_015255025.1	s__Haemophilus_D sp015255025	93.8571	430	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
GCA_905207935.1	s__Haemophilus_D sp905207935	93.8416	486	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215245.1	s__Haemophilus_D sp905215245	93.7241	425	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCF_003252725.1	s__Haemophilus_D parainfluenzae_L	93.5132	590	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.33	95.18	0.90	0.88	7	-
GCF_014931275.1	s__Haemophilus_D sp900755445	93.1744	601	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	93.0838	564	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCA_905205995.1	s__Haemophilus_D sp905205995	92.8985	556	715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:45,018] [INFO] GTDB search result was written to GCF_900450845.1_45473_E02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:45,019] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:45,023] [INFO] DFAST_QC result json was written to GCF_900450845.1_45473_E02_genomic.fna/dqc_result.json
[2024-01-25 19:45:45,023] [INFO] DFAST_QC completed!
[2024-01-25 19:45:45,023] [INFO] Total running time: 0h0m40s