[2024-01-24 12:31:03,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference
[2024-01-24 12:31:05,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,121] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,121] [INFO] Running command: gunzip -c /var/lib/cwl/stgddfedd0c-be80-4a3a-b0a9-10caf5800057/GCF_902150035.1_P9525_genomic.fna.gz | prodigal -d GCF_902150035.1_P9525_genomic.fna/cds.fna -a GCF_902150035.1_P9525_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:11,471] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:11,471] [INFO] Task started: HMMsearch
[2024-01-24 12:31:11,472] [INFO] Running command: hmmsearch --tblout GCF_902150035.1_P9525_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference/reference_markers.hmm GCF_902150035.1_P9525_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:11,691] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:11,693] [INFO] Found 6/6 markers.
[2024-01-24 12:31:11,717] [INFO] Query marker FASTA was written to GCF_902150035.1_P9525_genomic.fna/markers.fasta
[2024-01-24 12:31:11,718] [INFO] Task started: Blastn
[2024-01-24 12:31:11,718] [INFO] Running command: blastn -query GCF_902150035.1_P9525_genomic.fna/markers.fasta -db /var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference/reference_markers.fasta -out GCF_902150035.1_P9525_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:12,455] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:12,462] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:12,462] [INFO] Target genome list was writen to GCF_902150035.1_P9525_genomic.fna/target_genomes.txt
[2024-01-24 12:31:12,470] [INFO] Task started: fastANI
[2024-01-24 12:31:12,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgddfedd0c-be80-4a3a-b0a9-10caf5800057/GCF_902150035.1_P9525_genomic.fna.gz --refList GCF_902150035.1_P9525_genomic.fna/target_genomes.txt --output GCF_902150035.1_P9525_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:17,267] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:17,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:17,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:17,282] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:17,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:17,283] [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
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	100.0	723	725	95	conclusive
Enorma phocaeensis	strain=Marseille-P3242	GCA_900186505.1	1871019	1871019	type	True	85.8008	541	725	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	84.0912	424	725	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	81.9994	390	725	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	81.9145	383	725	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.904	307	725	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.7642	314	725	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.6884	320	725	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	80.6204	283	725	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.3201	227	725	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	78.4567	149	725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:17,284] [INFO] DFAST Taxonomy check result was written to GCF_902150035.1_P9525_genomic.fna/tc_result.tsv
[2024-01-24 12:31:17,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:17,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:17,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference/checkm_data
[2024-01-24 12:31:17,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:17,316] [INFO] Task started: CheckM
[2024-01-24 12:31:17,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902150035.1_P9525_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902150035.1_P9525_genomic.fna/checkm_input GCF_902150035.1_P9525_genomic.fna/checkm_result
[2024-01-24 12:31:40,504] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:40,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:40,527] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:40,527] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:40,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902150035.1_P9525_genomic.fna/markers.fasta)
[2024-01-24 12:31:40,528] [INFO] Task started: Blastn
[2024-01-24 12:31:40,528] [INFO] Running command: blastn -query GCF_902150035.1_P9525_genomic.fna/markers.fasta -db /var/lib/cwl/stg24a76a7d-190d-41d1-9676-131425334810/dqc_reference/reference_markers_gtdb.fasta -out GCF_902150035.1_P9525_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:41,829] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:41,833] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:41,834] [INFO] Target genome list was writen to GCF_902150035.1_P9525_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:41,883] [INFO] Task started: fastANI
[2024-01-24 12:31:41,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgddfedd0c-be80-4a3a-b0a9-10caf5800057/GCF_902150035.1_P9525_genomic.fna.gz --refList GCF_902150035.1_P9525_genomic.fna/target_genomes_gtdb.txt --output GCF_902150035.1_P9525_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:47,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:47,842] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:47,842] [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_902150035.1	s__Enorma burkinafasonensis	100.0	723	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900186505.1	s__Enorma phocaeensis	85.8003	541	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333815.1	s__Enorma sp000333815	84.2639	409	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	98.98	97.01	0.95	0.87	4	-
GCA_019117005.1	s__Collinsella stercoripullorum	82.2149	358	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCA_905210055.1	s__Enorma sp900751795	82.0863	320	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	99.77	99.77	0.84	0.84	2	-
GCF_002159765.1	s__Coprousia sp002159765	81.9079	367	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	97.90	97.74	0.89	0.88	3	-
GCF_000311845.1	s__Enorma massiliensis	81.8955	384	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Enorma	95.0	97.43	96.04	0.89	0.84	11	-
GCF_016900375.1	s__Collinsella sp002305035	81.6061	365	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.55	95.55	0.87	0.87	2	-
GCA_018715125.1	s__Coprousia avicola	81.3673	368	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901575.1	s__Limicola phocaeensis_A	81.3638	340	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160065.1	s__Limicola sp002160065	81.1993	338	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Limicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062655.1	s__Collinsella sp015062655	80.8038	315	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014645.1	s__Collinsella sp008014645	80.2837	265	725	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:47,844] [INFO] GTDB search result was written to GCF_902150035.1_P9525_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:47,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:47,848] [INFO] DFAST_QC result json was written to GCF_902150035.1_P9525_genomic.fna/dqc_result.json
[2024-01-24 12:31:47,848] [INFO] DFAST_QC completed!
[2024-01-24 12:31:47,848] [INFO] Total running time: 0h0m44s