[2023-06-08 12:31:40,215] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:31:40,221] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:31:40,221] [INFO] DQC Reference Directory: /var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference
[2023-06-08 12:31:41,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:31:41,530] [INFO] Task started: Prodigal
[2023-06-08 12:31:41,530] [INFO] Running command: gunzip -c /var/lib/cwl/stgdae295b1-63d0-40a3-9721-0a73a5d9a24c/GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna.gz | prodigal -d GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/cds.fna -a GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:31:46,967] [INFO] Task succeeded: Prodigal
[2023-06-08 12:31:46,967] [INFO] Task started: HMMsearch
[2023-06-08 12:31:46,968] [INFO] Running command: hmmsearch --tblout GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference/reference_markers.hmm GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:31:47,212] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:31:47,214] [INFO] Found 6/6 markers.
[2023-06-08 12:31:47,241] [INFO] Query marker FASTA was written to GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/markers.fasta
[2023-06-08 12:31:47,241] [INFO] Task started: Blastn
[2023-06-08 12:31:47,241] [INFO] Running command: blastn -query GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference/reference_markers.fasta -out GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:48,019] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:48,024] [INFO] Selected 22 target genomes.
[2023-06-08 12:31:48,025] [INFO] Target genome list was writen to GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/target_genomes.txt
[2023-06-08 12:31:48,032] [INFO] Task started: fastANI
[2023-06-08 12:31:48,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae295b1-63d0-40a3-9721-0a73a5d9a24c/GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna.gz --refList GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/target_genomes.txt --output GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:32:00,023] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:00,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:32:00,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:32:00,038] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 12:32:00,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 12:32:00,038] [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
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	98.6106	626	648	95	conclusive
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	78.7848	158	648	95	below_threshold
Rothia mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	78.2078	120	648	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	77.7322	69	648	95	below_threshold
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	77.7322	69	648	95	below_threshold
Kocuria carniphila	strain=CCM 132	GCA_004136555.1	262208	262208	type	True	76.6289	57	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:32:00,041] [INFO] DFAST Taxonomy check result was written to GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/tc_result.tsv
[2023-06-08 12:32:00,041] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:32:00,042] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:32:00,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference/checkm_data
[2023-06-08 12:32:00,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:32:00,070] [INFO] Task started: CheckM
[2023-06-08 12:32:00,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/checkm_input GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/checkm_result
[2023-06-08 12:32:23,132] [INFO] Task succeeded: CheckM
[2023-06-08 12:32:23,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:32:23,155] [INFO] ===== Completeness check finished =====
[2023-06-08 12:32:23,155] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:32:23,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/markers.fasta)
[2023-06-08 12:32:23,156] [INFO] Task started: Blastn
[2023-06-08 12:32:23,156] [INFO] Running command: blastn -query GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70fe5e0-00dd-4ef9-aa80-0a0e135c80c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:32:24,227] [INFO] Task succeeded: Blastn
[2023-06-08 12:32:24,232] [INFO] Selected 16 target genomes.
[2023-06-08 12:32:24,232] [INFO] Target genome list was writen to GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:32:24,281] [INFO] Task started: fastANI
[2023-06-08 12:32:24,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae295b1-63d0-40a3-9721-0a73a5d9a24c/GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna.gz --refList GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/target_genomes_gtdb.txt --output GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:32:31,835] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:31,847] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:32:31,847] [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_012396615.1	s__Rothia terrae	98.6106	626	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.55	98.48	0.95	0.93	4	conclusive
GCF_016924835.1	s__Rothia sp016924835	79.5266	238	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.38	99.38	0.96	0.96	2	-
GCF_014635585.1	s__Rothia aerolata	78.841	156	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418375.1	s__Rothia sp002418375	78.2327	142	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.17	96.17	0.93	0.93	2	-
GCA_015265375.1	s__Rothia sp015265375	78.1481	111	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
GCF_001061665.1	s__Rothia mucilaginosa_A	78.1117	93	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_001548235.1	s__Rothia mucilaginosa_B	78.0852	122	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	-
GCA_019115985.1	s__Rothia avicola	78.0414	146	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004569295.1	s__Rothia nasimurium_B	78.0212	154	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001808955.1	s__Rothia sp001808955	78.0171	123	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCF_014217215.1	s__Rothia nasimurium_C	77.9701	159	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.36	98.36	0.95	0.95	2	-
GCF_002087015.1	s__Rothia nasimurium_A	77.782	129	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901875305.1	s__Rothia sp902373285	77.6744	114	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	-
GCF_004136555.1	s__Kocuria carniphila	76.6648	56	648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.73	97.73	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-08 12:32:31,849] [INFO] GTDB search result was written to GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/result_gtdb.tsv
[2023-06-08 12:32:31,850] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:32:31,854] [INFO] DFAST_QC result json was written to GCA_902461355.1_UHGG-TPA_MGYG-HGUT-00326_genomic.fna/dqc_result.json
[2023-06-08 12:32:31,854] [INFO] DFAST_QC completed!
[2023-06-08 12:32:31,854] [INFO] Total running time: 0h0m52s