[2023-06-08 04:30:36,746] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:30:36,748] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:30:36,749] [INFO] DQC Reference Directory: /var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference
[2023-06-08 04:30:38,097] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:30:38,098] [INFO] Task started: Prodigal
[2023-06-08 04:30:38,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg57de9767-fddd-4a39-882d-65bf9a159c3a/GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:30:42,652] [INFO] Task succeeded: Prodigal
[2023-06-08 04:30:42,653] [INFO] Task started: HMMsearch
[2023-06-08 04:30:42,653] [INFO] Running command: hmmsearch --tblout GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference/reference_markers.hmm GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:30:42,889] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:30:42,891] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg57de9767-fddd-4a39-882d-65bf9a159c3a/GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 04:30:42,918] [INFO] Query marker FASTA was written to GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 04:30:42,919] [INFO] Task started: Blastn
[2023-06-08 04:30:42,919] [INFO] Running command: blastn -query GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference/reference_markers.fasta -out GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:43,523] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:43,530] [INFO] Selected 10 target genomes.
[2023-06-08 04:30:43,530] [INFO] Target genome list was writen to GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 04:30:43,563] [INFO] Task started: fastANI
[2023-06-08 04:30:43,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg57de9767-fddd-4a39-882d-65bf9a159c3a/GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:30:50,242] [INFO] Task succeeded: fastANI
[2023-06-08 04:30:50,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:30:50,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:30:50,248] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:30:50,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 04:30:50,249] [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
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	79.1628	158	467	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	79.0678	218	467	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	77.4775	51	467	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	77.4775	51	467	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:30:50,251] [INFO] DFAST Taxonomy check result was written to GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 04:30:50,251] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:30:50,251] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:30:50,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference/checkm_data
[2023-06-08 04:30:50,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:30:50,278] [INFO] Task started: CheckM
[2023-06-08 04:30:50,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 04:31:10,856] [INFO] Task succeeded: CheckM
[2023-06-08 04:31:10,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:31:10,879] [INFO] ===== Completeness check finished =====
[2023-06-08 04:31:10,879] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:31:10,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 04:31:10,880] [INFO] Task started: Blastn
[2023-06-08 04:31:10,880] [INFO] Running command: blastn -query GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc86caed8-8682-4291-9634-4d661f20e51d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:31:11,769] [INFO] Task succeeded: Blastn
[2023-06-08 04:31:11,775] [INFO] Selected 9 target genomes.
[2023-06-08 04:31:11,775] [INFO] Target genome list was writen to GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:31:11,777] [INFO] Task started: fastANI
[2023-06-08 04:31:11,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg57de9767-fddd-4a39-882d-65bf9a159c3a/GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:31:16,140] [INFO] Task succeeded: fastANI
[2023-06-08 04:31:16,157] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:31:16,157] [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_900167415.1	s__Hallerella intestinalis	98.286	449	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Hallerella	95.0	98.54	97.77	0.90	0.85	4	conclusive
GCF_002797675.1	s__Hallerella succinigenes	79.1628	158	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Hallerella	95.0	98.45	98.31	0.94	0.94	3	-
GCF_003148885.1	s__Hallerella porci	79.0585	219	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Hallerella	95.0	99.70	99.62	0.96	0.94	3	-
GCA_002390045.1	s__Hallerella sp002390045	78.03	126	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Hallerella	95.0	98.56	98.06	0.86	0.80	4	-
GCA_017642335.1	s__Fibrobacter sp017642335	77.8441	60	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.30	98.30	0.90	0.90	2	-
GCA_017959225.1	s__Hallerella sp017959225	77.443	132	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Hallerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142475.1	s__Fibrobacter sp900142475	77.222	57	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.25	95.07	0.84	0.80	4	-
GCA_902794535.1	s__Fibrobacter succinogenes_O	76.9496	53	467	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:31:16,160] [INFO] GTDB search result was written to GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 04:31:16,160] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:31:16,165] [INFO] DFAST_QC result json was written to GCA_945492415.1_SRR7188235_bin.44_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 04:31:16,165] [INFO] DFAST_QC completed!
[2023-06-08 04:31:16,165] [INFO] Total running time: 0h0m39s