[2024-01-24 13:25:47,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,636] [INFO] DQC Reference Directory: /var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference
[2024-01-24 13:25:49,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,005] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg525e49c4-b49d-4647-a78a-722164c14e2e/GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/cds.fna -a GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:54,734] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:54,735] [INFO] Task started: HMMsearch
[2024-01-24 13:25:54,735] [INFO] Running command: hmmsearch --tblout GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference/reference_markers.hmm GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:54,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:54,982] [INFO] Found 6/6 markers.
[2024-01-24 13:25:55,006] [INFO] Query marker FASTA was written to GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:25:55,007] [INFO] Task started: Blastn
[2024-01-24 13:25:55,007] [INFO] Running command: blastn -query GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference/reference_markers.fasta -out GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:55,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:55,599] [INFO] Selected 15 target genomes.
[2024-01-24 13:25:55,599] [INFO] Target genome list was writen to GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:25:55,607] [INFO] Task started: fastANI
[2024-01-24 13:25:55,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg525e49c4-b49d-4647-a78a-722164c14e2e/GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna.gz --refList GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:03,294] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:03,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:03,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:03,306] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:03,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:03,307] [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 porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	100.0	818	820	95	conclusive
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	77.3808	84	820	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	77.0827	99	820	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	76.8659	98	820	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.78	72	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:03,309] [INFO] DFAST Taxonomy check result was written to GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:26:03,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:03,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:03,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference/checkm_data
[2024-01-24 13:26:03,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:03,341] [INFO] Task started: CheckM
[2024-01-24 13:26:03,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/checkm_input GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:26:26,443] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:26,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:26,466] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:26,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:26,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:26:26,467] [INFO] Task started: Blastn
[2024-01-24 13:26:26,467] [INFO] Running command: blastn -query GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga6560f6a-f68f-44e1-9eae-f8d4fdc48176/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:27,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:27,233] [INFO] Selected 24 target genomes.
[2024-01-24 13:26:27,233] [INFO] Target genome list was writen to GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:27,280] [INFO] Task started: fastANI
[2024-01-24 13:26:27,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg525e49c4-b49d-4647-a78a-722164c14e2e/GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna.gz --refList GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:37,978] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:37,999] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:37,999] [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_900167145.1	s__Treponema_D porcinum	100.0	818	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	conclusive
GCA_900769325.1	s__Treponema_D sp900769325	79.7262	175	820	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_900541945.1	s__Treponema_D sp900541945	77.8841	182	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.94	97.90	0.88	0.87	3	-
GCA_016293005.1	s__Treponema_D sp016293005	77.8299	116	820	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_016297405.1	s__Treponema_D sp016297405	77.7196	94	820	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_017392945.1	s__Treponema_D sp017392945	77.6414	124	820	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_002437725.1	s__Treponema_D sp002437725	77.518	114	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.48	98.76	0.93	0.84	13	-
GCA_900317625.1	s__Treponema_D sp900317625	77.5118	137	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
GCA_017470605.1	s__Treponema_D sp017470605	77.2381	116	820	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_002449305.1	s__Treponema_D sp002449305	77.1826	84	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.77	97.10	0.90	0.86	10	-
GCA_017386165.1	s__Treponema_D sp017386165	77.1191	94	820	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	77.1082	60	820	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_002478955.1	s__Treponema_D sp002478955	77.1075	155	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCA_014803985.1	s__Treponema_D sp014803985	76.8298	77	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.03	97.81	0.86	0.80	8	-
GCA_002350445.1	s__Treponema_D sp002350445	76.5406	62	820	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.37	99.37	0.88	0.88	2	-
GCA_017616165.1	s__Treponema_D sp017616165	76.4576	65	820	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_017449285.1	s__Treponema_D sp017449285	76.0341	63	820	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 13:26:38,001] [INFO] GTDB search result was written to GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:38,002] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:38,005] [INFO] DFAST_QC result json was written to GCF_900167145.1_IMG-taxon_2582581326_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:26:38,006] [INFO] DFAST_QC completed!
[2024-01-24 13:26:38,006] [INFO] Total running time: 0h0m50s