[2024-01-24 15:14:50,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:14:50,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:14:50,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference
[2024-01-24 15:14:51,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:14:51,491] [INFO] Task started: Prodigal
[2024-01-24 15:14:51,491] [INFO] Running command: gunzip -c /var/lib/cwl/stgd47f9443-8aa2-4bd7-a3dd-8ad44d0ae404/GCF_000712295.1_sjonesii4.0_genomic.fna.gz | prodigal -d GCF_000712295.1_sjonesii4.0_genomic.fna/cds.fna -a GCF_000712295.1_sjonesii4.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:14:57,990] [INFO] Task succeeded: Prodigal
[2024-01-24 15:14:57,991] [INFO] Task started: HMMsearch
[2024-01-24 15:14:57,991] [INFO] Running command: hmmsearch --tblout GCF_000712295.1_sjonesii4.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference/reference_markers.hmm GCF_000712295.1_sjonesii4.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:14:58,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:14:58,254] [INFO] Found 6/6 markers.
[2024-01-24 15:14:58,281] [INFO] Query marker FASTA was written to GCF_000712295.1_sjonesii4.0_genomic.fna/markers.fasta
[2024-01-24 15:14:58,281] [INFO] Task started: Blastn
[2024-01-24 15:14:58,281] [INFO] Running command: blastn -query GCF_000712295.1_sjonesii4.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference/reference_markers.fasta -out GCF_000712295.1_sjonesii4.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:14:58,923] [INFO] Task succeeded: Blastn
[2024-01-24 15:14:58,927] [INFO] Selected 7 target genomes.
[2024-01-24 15:14:58,928] [INFO] Target genome list was writen to GCF_000712295.1_sjonesii4.0_genomic.fna/target_genomes.txt
[2024-01-24 15:14:58,946] [INFO] Task started: fastANI
[2024-01-24 15:14:58,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgd47f9443-8aa2-4bd7-a3dd-8ad44d0ae404/GCF_000712295.1_sjonesii4.0_genomic.fna.gz --refList GCF_000712295.1_sjonesii4.0_genomic.fna/target_genomes.txt --output GCF_000712295.1_sjonesii4.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:15:03,231] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:03,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:15:03,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:15:03,238] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:15:03,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:15:03,239] [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	100.0	873	879	95	conclusive
Synergistes jonesii	strain=ATCC 49833	GCA_001757485.1	2754	2754	type	True	99.9491	830	879	95	conclusive
Synergistes jonesii	strain=78-1	GCA_001757465.1	2754	2754	type	True	99.9065	844	879	95	conclusive
Cloacibacillus evryensis	strain=DSM 19522	GCA_000585335.1	508460	508460	type	True	78.9684	322	879	95	below_threshold
Cloacibacillus porcorum	strain=CL-84	GCA_001701045.1	1197717	1197717	type	True	78.4907	319	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:15:03,240] [INFO] DFAST Taxonomy check result was written to GCF_000712295.1_sjonesii4.0_genomic.fna/tc_result.tsv
[2024-01-24 15:15:03,241] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:15:03,241] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:15:03,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference/checkm_data
[2024-01-24 15:15:03,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:15:03,274] [INFO] Task started: CheckM
[2024-01-24 15:15:03,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000712295.1_sjonesii4.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000712295.1_sjonesii4.0_genomic.fna/checkm_input GCF_000712295.1_sjonesii4.0_genomic.fna/checkm_result
[2024-01-24 15:15:28,050] [INFO] Task succeeded: CheckM
[2024-01-24 15:15:28,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:15:28,081] [INFO] ===== Completeness check finished =====
[2024-01-24 15:15:28,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:15:28,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000712295.1_sjonesii4.0_genomic.fna/markers.fasta)
[2024-01-24 15:15:28,082] [INFO] Task started: Blastn
[2024-01-24 15:15:28,082] [INFO] Running command: blastn -query GCF_000712295.1_sjonesii4.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg34368ad1-6e50-4b9f-9fd6-b5deedd076de/dqc_reference/reference_markers_gtdb.fasta -out GCF_000712295.1_sjonesii4.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:15:29,030] [INFO] Task succeeded: Blastn
[2024-01-24 15:15:29,034] [INFO] Selected 11 target genomes.
[2024-01-24 15:15:29,034] [INFO] Target genome list was writen to GCF_000712295.1_sjonesii4.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:15:29,044] [INFO] Task started: fastANI
[2024-01-24 15:15:29,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgd47f9443-8aa2-4bd7-a3dd-8ad44d0ae404/GCF_000712295.1_sjonesii4.0_genomic.fna.gz --refList GCF_000712295.1_sjonesii4.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000712295.1_sjonesii4.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:15:35,264] [INFO] Task succeeded: fastANI
[2024-01-24 15:15:35,274] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:15:35,275] [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_000712295.1	s__Synergistes jonesii	100.0	873	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	99.99	99.98	1.00	1.00	6	conclusive
GCA_017537925.1	s__Synergistes sp017537925	79.6299	318	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544635.1	s__Caccocola faecigallinarum	78.9916	240	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	96.54	96.25	0.92	0.91	3	-
GCF_000585335.1	s__Cloacibacillus evryensis	78.9882	322	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Cloacibacillus	95.0	98.47	98.41	0.85	0.85	4	-
GCA_016288355.1	s__Synergistes sp016288355	78.9425	221	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Synergistes	95.0	97.70	97.70	0.68	0.68	2	-
GCF_001701045.1	s__Cloacibacillus porcorum	78.4782	320	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Cloacibacillus	95.0	98.00	97.94	0.91	0.91	4	-
GCF_002159945.1	s__Caccocola sp002159945	78.3887	287	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716365.1	s__Caccocola faecipullorum	78.3137	210	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545755.1	s__Caccocola sp900545755	77.8466	238	879	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Caccocola	95.0	99.79	99.79	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:15:35,276] [INFO] GTDB search result was written to GCF_000712295.1_sjonesii4.0_genomic.fna/result_gtdb.tsv
[2024-01-24 15:15:35,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:15:35,280] [INFO] DFAST_QC result json was written to GCF_000712295.1_sjonesii4.0_genomic.fna/dqc_result.json
[2024-01-24 15:15:35,281] [INFO] DFAST_QC completed!
[2024-01-24 15:15:35,281] [INFO] Total running time: 0h0m45s