[2023-06-13 01:40:48,152] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:40:48,154] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:40:48,154] [INFO] DQC Reference Directory: /var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference
[2023-06-13 01:40:49,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:40:49,370] [INFO] Task started: Prodigal
[2023-06-13 01:40:49,370] [INFO] Running command: gunzip -c /var/lib/cwl/stg830fb255-1566-4f55-947c-4e22be4751ad/GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:40:54,022] [INFO] Task succeeded: Prodigal
[2023-06-13 01:40:54,022] [INFO] Task started: HMMsearch
[2023-06-13 01:40:54,022] [INFO] Running command: hmmsearch --tblout GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference/reference_markers.hmm GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:40:54,213] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:40:54,214] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg830fb255-1566-4f55-947c-4e22be4751ad/GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 01:40:54,236] [INFO] Query marker FASTA was written to GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 01:40:54,236] [INFO] Task started: Blastn
[2023-06-13 01:40:54,237] [INFO] Running command: blastn -query GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference/reference_markers.fasta -out GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:40:54,833] [INFO] Task succeeded: Blastn
[2023-06-13 01:40:54,836] [INFO] Selected 29 target genomes.
[2023-06-13 01:40:54,836] [INFO] Target genome list was writen to GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 01:40:54,839] [INFO] Task started: fastANI
[2023-06-13 01:40:54,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg830fb255-1566-4f55-947c-4e22be4751ad/GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:41:10,586] [INFO] Task succeeded: fastANI
[2023-06-13 01:41:10,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:41:10,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:41:10,592] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 01:41:10,592] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 01:41:10,593] [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
Oribacterium sinus	strain=DSM 17245	GCA_014202695.1	237576	237576	type	True	95.2483	527	594	95	conclusive
Oribacterium asaccharolyticum	strain=ACB7	GCA_000238075.1	1501332	1501332	type	True	80.6031	185	594	95	below_threshold
Oribacterium parvum	strain=ACB1	GCA_000238055.2	1501329	1501329	type	True	79.8977	195	594	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:41:10,594] [INFO] DFAST Taxonomy check result was written to GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 01:41:10,595] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:41:10,595] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:41:10,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference/checkm_data
[2023-06-13 01:41:10,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:41:10,622] [INFO] Task started: CheckM
[2023-06-13 01:41:10,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 01:41:30,614] [INFO] Task succeeded: CheckM
[2023-06-13 01:41:30,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.88%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:41:30,636] [INFO] ===== Completeness check finished =====
[2023-06-13 01:41:30,636] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:41:30,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 01:41:30,637] [INFO] Task started: Blastn
[2023-06-13 01:41:30,637] [INFO] Running command: blastn -query GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc510a568-6f13-4f43-9993-d9f51142562f/dqc_reference/reference_markers_gtdb.fasta -out GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:41:31,610] [INFO] Task succeeded: Blastn
[2023-06-13 01:41:31,613] [INFO] Selected 33 target genomes.
[2023-06-13 01:41:31,613] [INFO] Target genome list was writen to GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:41:31,626] [INFO] Task started: fastANI
[2023-06-13 01:41:31,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg830fb255-1566-4f55-947c-4e22be4751ad/GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:41:47,584] [INFO] Task succeeded: fastANI
[2023-06-13 01:41:47,589] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 01:41:47,590] [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_014202695.1	s__Oribacterium sinus	95.2483	527	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	95.41	95.16	0.92	0.89	5	conclusive
GCF_000238075.1	s__Oribacterium asaccharolyticum	80.6031	185	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	96.30	96.30	0.89	0.89	2	-
GCA_015258095.1	s__Oribacterium sp015258095	80.2989	120	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238055.2	s__Oribacterium parvum	79.8283	198	594	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium	95.0	98.88	98.13	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2023-06-13 01:41:47,593] [INFO] GTDB search result was written to GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 01:41:47,594] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:41:47,597] [INFO] DFAST_QC result json was written to GCA_938022235.1_SRR8114052_bin.33_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 01:41:47,597] [INFO] DFAST_QC completed!
[2023-06-13 01:41:47,597] [INFO] Total running time: 0h0m59s