[2023-06-28 12:33:34,343] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:33:34,347] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:33:34,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference
[2023-06-28 12:33:35,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:33:35,606] [INFO] Task started: Prodigal
[2023-06-28 12:33:35,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ce02678-6aa2-43b3-b2a1-150c68d8768c/GCA_017443445.1_ASM1744344v1_genomic.fna.gz | prodigal -d GCA_017443445.1_ASM1744344v1_genomic.fna/cds.fna -a GCA_017443445.1_ASM1744344v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:33:39,269] [INFO] Task succeeded: Prodigal
[2023-06-28 12:33:39,269] [INFO] Task started: HMMsearch
[2023-06-28 12:33:39,269] [INFO] Running command: hmmsearch --tblout GCA_017443445.1_ASM1744344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference/reference_markers.hmm GCA_017443445.1_ASM1744344v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:33:39,443] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:33:39,445] [INFO] Found 6/6 markers.
[2023-06-28 12:33:39,468] [INFO] Query marker FASTA was written to GCA_017443445.1_ASM1744344v1_genomic.fna/markers.fasta
[2023-06-28 12:33:39,468] [INFO] Task started: Blastn
[2023-06-28 12:33:39,468] [INFO] Running command: blastn -query GCA_017443445.1_ASM1744344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference/reference_markers.fasta -out GCA_017443445.1_ASM1744344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:33:40,028] [INFO] Task succeeded: Blastn
[2023-06-28 12:33:40,032] [INFO] Selected 8 target genomes.
[2023-06-28 12:33:40,032] [INFO] Target genome list was writen to GCA_017443445.1_ASM1744344v1_genomic.fna/target_genomes.txt
[2023-06-28 12:33:40,033] [INFO] Task started: fastANI
[2023-06-28 12:33:40,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce02678-6aa2-43b3-b2a1-150c68d8768c/GCA_017443445.1_ASM1744344v1_genomic.fna.gz --refList GCA_017443445.1_ASM1744344v1_genomic.fna/target_genomes.txt --output GCA_017443445.1_ASM1744344v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:33:43,470] [INFO] Task succeeded: fastANI
[2023-06-28 12:33:43,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:33:43,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:33:43,477] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:33:43,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:33:43,477] [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
Synergistes jonesii	strain=78-1	GCA_000712295.1	2754	2754	type	True	78.9807	208	435	95	below_threshold
Synergistes jonesii	strain=ATCC 49833	GCA_001757485.1	2754	2754	type	True	78.9413	208	435	95	below_threshold
Synergistes jonesii	strain=78-1	GCA_001757465.1	2754	2754	type	True	78.9405	207	435	95	below_threshold
Cloacibacillus evryensis	strain=DSM 19522	GCA_000585335.1	508460	508460	type	True	77.5636	118	435	95	below_threshold
Cloacibacillus porcorum	strain=CL-84	GCA_001701045.1	1197717	1197717	type	True	77.1602	116	435	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:33:43,479] [INFO] DFAST Taxonomy check result was written to GCA_017443445.1_ASM1744344v1_genomic.fna/tc_result.tsv
[2023-06-28 12:33:43,480] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:33:43,480] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:33:43,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference/checkm_data
[2023-06-28 12:33:43,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:33:43,501] [INFO] Task started: CheckM
[2023-06-28 12:33:43,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017443445.1_ASM1744344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017443445.1_ASM1744344v1_genomic.fna/checkm_input GCA_017443445.1_ASM1744344v1_genomic.fna/checkm_result
[2023-06-28 12:34:01,031] [INFO] Task succeeded: CheckM
[2023-06-28 12:34:01,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:34:01,047] [INFO] ===== Completeness check finished =====
[2023-06-28 12:34:01,047] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:34:01,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017443445.1_ASM1744344v1_genomic.fna/markers.fasta)
[2023-06-28 12:34:01,047] [INFO] Task started: Blastn
[2023-06-28 12:34:01,048] [INFO] Running command: blastn -query GCA_017443445.1_ASM1744344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f7701e9-0215-4125-b53e-c19554aed185/dqc_reference/reference_markers_gtdb.fasta -out GCA_017443445.1_ASM1744344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:01,887] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:01,891] [INFO] Selected 16 target genomes.
[2023-06-28 12:34:01,891] [INFO] Target genome list was writen to GCA_017443445.1_ASM1744344v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:34:01,894] [INFO] Task started: fastANI
[2023-06-28 12:34:01,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ce02678-6aa2-43b3-b2a1-150c68d8768c/GCA_017443445.1_ASM1744344v1_genomic.fna.gz --refList GCA_017443445.1_ASM1744344v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017443445.1_ASM1744344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:34:08,376] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:08,384] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:34:08,384] [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_016288355.1	s__Synergistes sp016288355	97.7021	297	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	97.70	97.70	0.68	0.68	2	conclusive
GCA_017537925.1	s__Synergistes sp017537925	86.2288	339	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712295.1	s__Synergistes jonesii	78.9807	208	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	99.99	99.98	1.00	1.00	6	-
GCF_000585335.1	s__Cloacibacillus evryensis	77.5636	118	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Cloacibacillus	95.0	98.47	98.41	0.85	0.85	4	-
GCA_900544635.1	s__Caccocola faecigallinarum	77.2926	80	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	96.54	96.25	0.92	0.91	3	-
GCA_900545755.1	s__Caccocola sp900545755	77.2521	81	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	99.79	99.79	0.89	0.89	2	-
GCF_001701045.1	s__Cloacibacillus porcorum	77.1602	116	435	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Cloacibacillus	95.0	98.00	97.94	0.91	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-28 12:34:08,386] [INFO] GTDB search result was written to GCA_017443445.1_ASM1744344v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:34:08,386] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:34:08,389] [INFO] DFAST_QC result json was written to GCA_017443445.1_ASM1744344v1_genomic.fna/dqc_result.json
[2023-06-28 12:34:08,389] [INFO] DFAST_QC completed!
[2023-06-28 12:34:08,389] [INFO] Total running time: 0h0m34s