[2023-06-13 23:18:02,540] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:18:02,549] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:18:02,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference
[2023-06-13 23:18:04,362] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:18:04,362] [INFO] Task started: Prodigal
[2023-06-13 23:18:04,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg4eaa45e0-b6a3-4935-acb3-9053fdf491f2/GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:18:10,315] [INFO] Task succeeded: Prodigal
[2023-06-13 23:18:10,315] [INFO] Task started: HMMsearch
[2023-06-13 23:18:10,315] [INFO] Running command: hmmsearch --tblout GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference/reference_markers.hmm GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:18:10,575] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:18:10,576] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4eaa45e0-b6a3-4935-acb3-9053fdf491f2/GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 23:18:10,607] [INFO] Query marker FASTA was written to GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 23:18:10,607] [INFO] Task started: Blastn
[2023-06-13 23:18:10,607] [INFO] Running command: blastn -query GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference/reference_markers.fasta -out GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:18:11,162] [INFO] Task succeeded: Blastn
[2023-06-13 23:18:11,165] [INFO] Selected 28 target genomes.
[2023-06-13 23:18:11,166] [INFO] Target genome list was writen to GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 23:18:11,167] [INFO] Task started: fastANI
[2023-06-13 23:18:11,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg4eaa45e0-b6a3-4935-acb3-9053fdf491f2/GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:18:25,277] [INFO] Task succeeded: fastANI
[2023-06-13 23:18:25,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:18:25,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:18:25,281] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:18:25,281] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 23:18:25,281] [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
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	77.1043	57	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 23:18:25,283] [INFO] DFAST Taxonomy check result was written to GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 23:18:25,283] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:18:25,283] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:18:25,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference/checkm_data
[2023-06-13 23:18:25,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:18:25,323] [INFO] Task started: CheckM
[2023-06-13 23:18:25,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 23:18:47,948] [INFO] Task succeeded: CheckM
[2023-06-13 23:18:47,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:18:47,968] [INFO] ===== Completeness check finished =====
[2023-06-13 23:18:47,969] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:18:47,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 23:18:47,970] [INFO] Task started: Blastn
[2023-06-13 23:18:47,970] [INFO] Running command: blastn -query GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg157781d7-a207-4861-91d4-8cfaa3afb7aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:18:48,769] [INFO] Task succeeded: Blastn
[2023-06-13 23:18:48,772] [INFO] Selected 7 target genomes.
[2023-06-13 23:18:48,772] [INFO] Target genome list was writen to GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:18:48,773] [INFO] Task started: fastANI
[2023-06-13 23:18:48,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg4eaa45e0-b6a3-4935-acb3-9053fdf491f2/GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:18:55,300] [INFO] Task succeeded: fastANI
[2023-06-13 23:18:55,305] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 23:18:55,305] [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
GCA_910588655.1	s__Butyribacter sp910588655	99.1125	934	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910579085.1	s__Butyribacter sp910579085	91.982	855	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910580005.1	s__Butyribacter sp910580005	88.6004	647	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499945.1	s__Butyribacter sp002499945	83.6777	639	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586555.1	s__Butyribacter sp910586555	83.4819	678	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577825.1	s__Butyribacter sp910577825	83.2116	666	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774235.1	s__Butyribacter sp009774235	81.496	616	1067	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	99.07	99.07	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-13 23:18:55,307] [INFO] GTDB search result was written to GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 23:18:55,308] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:18:55,310] [INFO] DFAST_QC result json was written to GCA_947568175.1_SRR19759462_bin.50_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 23:18:55,310] [INFO] DFAST_QC completed!
[2023-06-13 23:18:55,310] [INFO] Total running time: 0h0m53s