[2023-06-30 15:58:24,171] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:58:24,173] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:58:24,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference
[2023-06-30 15:58:25,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:58:25,326] [INFO] Task started: Prodigal
[2023-06-30 15:58:25,326] [INFO] Running command: gunzip -c /var/lib/cwl/stga26cb9a0-f1ac-4084-af7f-390f1557d722/GCA_016901295.1_ASM1690129v1_genomic.fna.gz | prodigal -d GCA_016901295.1_ASM1690129v1_genomic.fna/cds.fna -a GCA_016901295.1_ASM1690129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:58:30,401] [INFO] Task succeeded: Prodigal
[2023-06-30 15:58:30,401] [INFO] Task started: HMMsearch
[2023-06-30 15:58:30,401] [INFO] Running command: hmmsearch --tblout GCA_016901295.1_ASM1690129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference/reference_markers.hmm GCA_016901295.1_ASM1690129v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:58:30,590] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:58:30,591] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga26cb9a0-f1ac-4084-af7f-390f1557d722/GCA_016901295.1_ASM1690129v1_genomic.fna.gz]
[2023-06-30 15:58:30,611] [INFO] Query marker FASTA was written to GCA_016901295.1_ASM1690129v1_genomic.fna/markers.fasta
[2023-06-30 15:58:30,611] [INFO] Task started: Blastn
[2023-06-30 15:58:30,611] [INFO] Running command: blastn -query GCA_016901295.1_ASM1690129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference/reference_markers.fasta -out GCA_016901295.1_ASM1690129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:58:31,229] [INFO] Task succeeded: Blastn
[2023-06-30 15:58:31,232] [INFO] Selected 14 target genomes.
[2023-06-30 15:58:31,233] [INFO] Target genome list was writen to GCA_016901295.1_ASM1690129v1_genomic.fna/target_genomes.txt
[2023-06-30 15:58:31,234] [INFO] Task started: fastANI
[2023-06-30 15:58:31,234] [INFO] Running command: fastANI --query /var/lib/cwl/stga26cb9a0-f1ac-4084-af7f-390f1557d722/GCA_016901295.1_ASM1690129v1_genomic.fna.gz --refList GCA_016901295.1_ASM1690129v1_genomic.fna/target_genomes.txt --output GCA_016901295.1_ASM1690129v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:58:40,455] [INFO] Task succeeded: fastANI
[2023-06-30 15:58:40,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:58:40,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:58:40,463] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:58:40,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:58:40,463] [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
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	80.8935	266	571	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.8057	228	571	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.7518	237	571	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.7472	230	571	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.5687	190	571	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.4119	200	571	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.9095	187	571	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	78.5586	208	571	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	77.9292	160	571	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:58:40,465] [INFO] DFAST Taxonomy check result was written to GCA_016901295.1_ASM1690129v1_genomic.fna/tc_result.tsv
[2023-06-30 15:58:40,465] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:58:40,466] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:58:40,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference/checkm_data
[2023-06-30 15:58:40,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:58:40,490] [INFO] Task started: CheckM
[2023-06-30 15:58:40,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016901295.1_ASM1690129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016901295.1_ASM1690129v1_genomic.fna/checkm_input GCA_016901295.1_ASM1690129v1_genomic.fna/checkm_result
[2023-06-30 15:58:59,548] [INFO] Task succeeded: CheckM
[2023-06-30 15:58:59,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 15:58:59,567] [INFO] ===== Completeness check finished =====
[2023-06-30 15:58:59,567] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:58:59,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016901295.1_ASM1690129v1_genomic.fna/markers.fasta)
[2023-06-30 15:58:59,568] [INFO] Task started: Blastn
[2023-06-30 15:58:59,568] [INFO] Running command: blastn -query GCA_016901295.1_ASM1690129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73e47001-4bbe-4c19-8928-3d07861ac42f/dqc_reference/reference_markers_gtdb.fasta -out GCA_016901295.1_ASM1690129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:59:00,512] [INFO] Task succeeded: Blastn
[2023-06-30 15:59:00,516] [INFO] Selected 12 target genomes.
[2023-06-30 15:59:00,516] [INFO] Target genome list was writen to GCA_016901295.1_ASM1690129v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:59:00,522] [INFO] Task started: fastANI
[2023-06-30 15:59:00,522] [INFO] Running command: fastANI --query /var/lib/cwl/stga26cb9a0-f1ac-4084-af7f-390f1557d722/GCA_016901295.1_ASM1690129v1_genomic.fna.gz --refList GCA_016901295.1_ASM1690129v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016901295.1_ASM1690129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:59:05,687] [INFO] Task succeeded: fastANI
[2023-06-30 15:59:05,695] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 15:59:05,695] [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_900105025.1	s__Parafannyhessea umbonata	97.504	529	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	95.62	95.16	0.88	0.79	34	conclusive
GCF_012844235.1	s__Parafannyhessea sp900538935	93.4576	521	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCA_003862195.1	s__Parafannyhessea sp003862195	85.559	425	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_902780325.1	s__Parafannyhessea sp902787335	81.0416	216	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCA_905214865.1	s__Olsenella_H sp905214865	80.4794	279	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	99.90	99.90	0.96	0.96	2	-
GCF_009695875.1	s__Olsenella_H porci	80.1426	263	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_H	95.0	97.87	97.72	0.91	0.87	6	-
GCF_900111255.1	s__Parafannyhessea umbonata_A	79.9806	268	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	99.32	99.30	0.95	0.94	4	-
GCF_000143845.1	s__Olsenella uli	79.8057	228	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCF_900120385.1	s__Olsenella_I phocaeensis	79.7524	237	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_I	95.0	97.88	97.64	0.87	0.85	3	-
GCF_900155635.1	s__Olsenella_G urininfantis	79.5687	190	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305995.1	s__UBA1367 sp002305995	78.6491	160	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017459925.1	s__UBA9715 sp017459925	77.0395	54	571	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:59:05,697] [INFO] GTDB search result was written to GCA_016901295.1_ASM1690129v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:59:05,698] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:59:05,701] [INFO] DFAST_QC result json was written to GCA_016901295.1_ASM1690129v1_genomic.fna/dqc_result.json
[2023-06-30 15:59:05,701] [INFO] DFAST_QC completed!
[2023-06-30 15:59:05,701] [INFO] Total running time: 0h0m42s