[2023-06-08 13:52:31,913] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:52:31,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:52:31,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference
[2023-06-08 13:52:33,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:52:33,193] [INFO] Task started: Prodigal
[2023-06-08 13:52:33,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg87e45d8e-832e-4596-8592-629822f0c626/GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna.gz | prodigal -d GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/cds.fna -a GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:52:37,950] [INFO] Task succeeded: Prodigal
[2023-06-08 13:52:37,950] [INFO] Task started: HMMsearch
[2023-06-08 13:52:37,950] [INFO] Running command: hmmsearch --tblout GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference/reference_markers.hmm GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:52:38,210] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:52:38,211] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87e45d8e-832e-4596-8592-629822f0c626/GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna.gz]
[2023-06-08 13:52:38,241] [INFO] Query marker FASTA was written to GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/markers.fasta
[2023-06-08 13:52:38,241] [INFO] Task started: Blastn
[2023-06-08 13:52:38,242] [INFO] Running command: blastn -query GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/markers.fasta -db /var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference/reference_markers.fasta -out GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:38,944] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:38,949] [INFO] Selected 12 target genomes.
[2023-06-08 13:52:38,949] [INFO] Target genome list was writen to GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/target_genomes.txt
[2023-06-08 13:52:38,951] [INFO] Task started: fastANI
[2023-06-08 13:52:38,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e45d8e-832e-4596-8592-629822f0c626/GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna.gz --refList GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/target_genomes.txt --output GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:52:45,691] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:45,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:52:45,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:52:45,704] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2023-06-08 13:52:45,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 13:52:45,704] [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	95.532	627	708	95	conclusive
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	95.5202	629	708	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	95.5071	620	708	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	95.4706	631	708	95	conclusive
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	82.7263	347	708	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	82.2736	352	708	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.9917	319	708	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	78.5599	286	708	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:52:45,706] [INFO] DFAST Taxonomy check result was written to GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/tc_result.tsv
[2023-06-08 13:52:45,707] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:52:45,708] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:52:45,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference/checkm_data
[2023-06-08 13:52:45,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:52:45,733] [INFO] Task started: CheckM
[2023-06-08 13:52:45,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/checkm_input GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/checkm_result
[2023-06-08 13:53:07,108] [INFO] Task succeeded: CheckM
[2023-06-08 13:53:07,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:53:07,128] [INFO] ===== Completeness check finished =====
[2023-06-08 13:53:07,129] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:53:07,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/markers.fasta)
[2023-06-08 13:53:07,129] [INFO] Task started: Blastn
[2023-06-08 13:53:07,130] [INFO] Running command: blastn -query GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/markers.fasta -db /var/lib/cwl/stg19db987f-e12a-4153-a798-c4f820b6ccd4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:53:08,168] [INFO] Task succeeded: Blastn
[2023-06-08 13:53:08,172] [INFO] Selected 15 target genomes.
[2023-06-08 13:53:08,172] [INFO] Target genome list was writen to GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:53:08,173] [INFO] Task started: fastANI
[2023-06-08 13:53:08,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e45d8e-832e-4596-8592-629822f0c626/GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna.gz --refList GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/target_genomes_gtdb.txt --output GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:53:14,999] [INFO] Task succeeded: fastANI
[2023-06-08 13:53:15,017] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:53:15,017] [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	95.4706	631	708	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	94.4629	588	708	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	94.2701	502	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCA_900756155.1	s__Haemophilus_D sp900756155	93.9533	573	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCF_001815355.1	s__Haemophilus_D sp001815355	93.9388	569	708	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_905215245.1	s__Haemophilus_D sp905215245	93.8957	407	708	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_000210895.1	s__Haemophilus_D parainfluenzae_A	93.8411	585	708	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_014931275.1	s__Haemophilus_D sp900755445	93.7997	585	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCA_905207935.1	s__Haemophilus_D sp905207935	93.7701	486	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003252725.1	s__Haemophilus_D parainfluenzae_L	93.7489	587	708	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_003253005.1	s__Haemophilus_D parainfluenzae_M	93.716	576	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCF_001679485.1	s__Haemophilus_D sp001679485	93.5754	573	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	95.82	95.82	0.90	0.90	2	-
GCA_900756875.1	s__Haemophilus_D sp900756875	93.3374	452	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
GCA_905205995.1	s__Haemophilus_D sp905205995	93.2908	546	708	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_018381425.1	s__Haemophilus_D parainfluenzae_O	93.036	350	708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
--------------------------------------------------------------------------------
[2023-06-08 13:53:15,020] [INFO] GTDB search result was written to GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/result_gtdb.tsv
[2023-06-08 13:53:15,021] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:53:15,027] [INFO] DFAST_QC result json was written to GCA_902461185.1_UHGG-TPA_MGYG-HGUT-00317_genomic.fna/dqc_result.json
[2023-06-08 13:53:15,027] [INFO] DFAST_QC completed!
[2023-06-08 13:53:15,028] [INFO] Total running time: 0h0m43s