[2024-01-24 15:18:25,891] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:25,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:25,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference
[2024-01-24 15:18:27,228] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,229] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,229] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe29f0e9-d0b3-4011-bfb4-cde96fcd6b2c/GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/cds.fna -a GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:32,868] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:32,869] [INFO] Task started: HMMsearch
[2024-01-24 15:18:32,869] [INFO] Running command: hmmsearch --tblout GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference/reference_markers.hmm GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:33,118] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:33,119] [INFO] Found 6/6 markers.
[2024-01-24 15:18:33,141] [INFO] Query marker FASTA was written to GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:18:33,141] [INFO] Task started: Blastn
[2024-01-24 15:18:33,141] [INFO] Running command: blastn -query GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference/reference_markers.fasta -out GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:33,736] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:33,739] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:33,739] [INFO] Target genome list was writen to GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:18:33,767] [INFO] Task started: fastANI
[2024-01-24 15:18:33,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe29f0e9-d0b3-4011-bfb4-cde96fcd6b2c/GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna.gz --refList GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:41,838] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:41,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:41,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:41,845] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:41,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:41,846] [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
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	100.0	816	821	95	conclusive
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	80.9562	141	821	95	below_threshold
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	78.0517	95	821	95	below_threshold
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	77.622	125	821	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	77.5454	98	821	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:41,847] [INFO] DFAST Taxonomy check result was written to GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:18:41,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:41,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:41,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference/checkm_data
[2024-01-24 15:18:41,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:41,876] [INFO] Task started: CheckM
[2024-01-24 15:18:41,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/checkm_input GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:19:06,203] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:06,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,226] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:06,227] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:06,227] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:19:06,228] [INFO] Task started: Blastn
[2024-01-24 15:19:06,228] [INFO] Running command: blastn -query GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d85f99-96bc-4768-b5bd-af4598c78d49/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:07,066] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:07,069] [INFO] Selected 16 target genomes.
[2024-01-24 15:19:07,069] [INFO] Target genome list was writen to GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:07,084] [INFO] Task started: fastANI
[2024-01-24 15:19:07,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe29f0e9-d0b3-4011-bfb4-cde96fcd6b2c/GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna.gz --refList GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:14,755] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:14,774] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:14,774] [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_900167025.1	s__Treponema_D berlinense	100.0	816	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.85	98.81	0.93	0.90	4	conclusive
GCA_002477955.1	s__Treponema_D sp002477955	93.4813	627	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.57	99.37	0.91	0.86	7	-
GCA_900770075.1	s__Treponema_D sp900770075	79.9991	371	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.11	97.11	0.86	0.86	2	-
GCA_002404895.1	s__Treponema_D sp002404895	79.0506	178	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283615.1	s__Treponema_D sp016283615	78.3527	192	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900497595.1	s__Treponema_D pectinovorum	77.8557	229	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.09	98.00	0.96	0.94	5	-
GCA_017469785.1	s__Treponema_D sp017469785	77.7222	99	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.36	97.36	0.82	0.82	2	-
GCA_003447785.1	s__Treponema_D sp003447785	77.5806	150	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.19	95.96	0.79	0.73	4	-
GCA_016296655.1	s__Treponema_D sp016296655	77.4662	108	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018064905.1	s__Treponema_D sp018064905	77.3406	131	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769325.1	s__Treponema_D sp900769325	77.3082	110	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286535.1	s__Treponema_D sp016286535	76.8565	87	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293005.1	s__Treponema_D sp016293005	76.7184	81	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.04	98.04	0.88	0.88	2	-
GCA_016286365.1	s__Treponema_D sp016286365	76.3482	83	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:14,775] [INFO] GTDB search result was written to GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:14,776] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:14,779] [INFO] DFAST_QC result json was written to GCF_900167025.1_IMG-taxon_2582581319_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:19:14,780] [INFO] DFAST_QC completed!
[2024-01-24 15:19:14,780] [INFO] Total running time: 0h0m49s