[2023-06-29 00:28:29,708] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:28:29,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:28:29,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference
[2023-06-29 00:28:30,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:28:30,908] [INFO] Task started: Prodigal
[2023-06-29 00:28:30,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg4704b965-8c2d-49a2-8f00-cf0938257511/GCA_017400155.1_ASM1740015v1_genomic.fna.gz | prodigal -d GCA_017400155.1_ASM1740015v1_genomic.fna/cds.fna -a GCA_017400155.1_ASM1740015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:28:39,561] [INFO] Task succeeded: Prodigal
[2023-06-29 00:28:39,562] [INFO] Task started: HMMsearch
[2023-06-29 00:28:39,562] [INFO] Running command: hmmsearch --tblout GCA_017400155.1_ASM1740015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference/reference_markers.hmm GCA_017400155.1_ASM1740015v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:28:39,773] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:28:39,774] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4704b965-8c2d-49a2-8f00-cf0938257511/GCA_017400155.1_ASM1740015v1_genomic.fna.gz]
[2023-06-29 00:28:39,816] [INFO] Query marker FASTA was written to GCA_017400155.1_ASM1740015v1_genomic.fna/markers.fasta
[2023-06-29 00:28:39,817] [INFO] Task started: Blastn
[2023-06-29 00:28:39,817] [INFO] Running command: blastn -query GCA_017400155.1_ASM1740015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference/reference_markers.fasta -out GCA_017400155.1_ASM1740015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:28:40,344] [INFO] Task succeeded: Blastn
[2023-06-29 00:28:40,347] [INFO] Selected 10 target genomes.
[2023-06-29 00:28:40,348] [INFO] Target genome list was writen to GCA_017400155.1_ASM1740015v1_genomic.fna/target_genomes.txt
[2023-06-29 00:28:40,349] [INFO] Task started: fastANI
[2023-06-29 00:28:40,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg4704b965-8c2d-49a2-8f00-cf0938257511/GCA_017400155.1_ASM1740015v1_genomic.fna.gz --refList GCA_017400155.1_ASM1740015v1_genomic.fna/target_genomes.txt --output GCA_017400155.1_ASM1740015v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:28:46,681] [INFO] Task succeeded: fastANI
[2023-06-29 00:28:46,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:28:46,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:28:46,688] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:28:46,688] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:28:46,688] [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
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	91.0912	631	855	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	91.0728	630	855	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	78.2146	129	855	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	77.0252	55	855	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:28:46,690] [INFO] DFAST Taxonomy check result was written to GCA_017400155.1_ASM1740015v1_genomic.fna/tc_result.tsv
[2023-06-29 00:28:46,691] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:28:46,691] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:28:46,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference/checkm_data
[2023-06-29 00:28:46,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:28:46,734] [INFO] Task started: CheckM
[2023-06-29 00:28:46,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017400155.1_ASM1740015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017400155.1_ASM1740015v1_genomic.fna/checkm_input GCA_017400155.1_ASM1740015v1_genomic.fna/checkm_result
[2023-06-29 00:29:16,667] [INFO] Task succeeded: CheckM
[2023-06-29 00:29:16,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.43%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 00:29:16,687] [INFO] ===== Completeness check finished =====
[2023-06-29 00:29:16,687] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:29:16,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017400155.1_ASM1740015v1_genomic.fna/markers.fasta)
[2023-06-29 00:29:16,688] [INFO] Task started: Blastn
[2023-06-29 00:29:16,688] [INFO] Running command: blastn -query GCA_017400155.1_ASM1740015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc722c09a-5e6a-4044-aa71-c0ec576153fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_017400155.1_ASM1740015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:29:17,391] [INFO] Task succeeded: Blastn
[2023-06-29 00:29:17,394] [INFO] Selected 7 target genomes.
[2023-06-29 00:29:17,394] [INFO] Target genome list was writen to GCA_017400155.1_ASM1740015v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:29:17,399] [INFO] Task started: fastANI
[2023-06-29 00:29:17,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg4704b965-8c2d-49a2-8f00-cf0938257511/GCA_017400155.1_ASM1740015v1_genomic.fna.gz --refList GCA_017400155.1_ASM1740015v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017400155.1_ASM1740015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:29:22,898] [INFO] Task succeeded: fastANI
[2023-06-29 00:29:22,906] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:29:22,906] [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_900177805.1	s__Fibrobacter sp900177805	95.7339	651	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.22	97.22	0.89	0.89	2	conclusive
GCA_902791475.1	s__Fibrobacter succinogenes_J	92.5084	632	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.39	95.39	0.76	0.76	2	-
GCF_900215325.1	s__Fibrobacter sp900215325	91.1537	616	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.50	97.09	0.94	0.94	6	-
GCF_000146505.1	s__Fibrobacter succinogenes	91.0823	630	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002210425.1	s__Fibrobacter elongatus	91.0012	629	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.37	97.19	0.91	0.89	4	-
GCA_002394865.1	s__Fibrobacter sp002394865	90.2341	616	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002210345.1	s__Fibrobacter sp002210345	88.6139	599	855	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.16	96.29	0.89	0.80	6	-
--------------------------------------------------------------------------------
[2023-06-29 00:29:22,908] [INFO] GTDB search result was written to GCA_017400155.1_ASM1740015v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:29:22,908] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:29:22,911] [INFO] DFAST_QC result json was written to GCA_017400155.1_ASM1740015v1_genomic.fna/dqc_result.json
[2023-06-29 00:29:22,911] [INFO] DFAST_QC completed!
[2023-06-29 00:29:22,911] [INFO] Total running time: 0h0m53s