[2024-01-24 13:45:59,344] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:59,346] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:59,346] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference
[2024-01-24 13:46:00,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,593] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg49f3d04b-81df-4a34-a3a0-e041f6075221/GCF_008153345.1_ASM815334v1_genomic.fna.gz | prodigal -d GCF_008153345.1_ASM815334v1_genomic.fna/cds.fna -a GCF_008153345.1_ASM815334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:08,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:08,517] [INFO] Task started: HMMsearch
[2024-01-24 13:46:08,518] [INFO] Running command: hmmsearch --tblout GCF_008153345.1_ASM815334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference/reference_markers.hmm GCF_008153345.1_ASM815334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:08,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:08,782] [INFO] Found 6/6 markers.
[2024-01-24 13:46:08,818] [INFO] Query marker FASTA was written to GCF_008153345.1_ASM815334v1_genomic.fna/markers.fasta
[2024-01-24 13:46:08,819] [INFO] Task started: Blastn
[2024-01-24 13:46:08,819] [INFO] Running command: blastn -query GCF_008153345.1_ASM815334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference/reference_markers.fasta -out GCF_008153345.1_ASM815334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:09,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:09,406] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:09,407] [INFO] Target genome list was writen to GCF_008153345.1_ASM815334v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:09,607] [INFO] Task started: fastANI
[2024-01-24 13:46:09,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg49f3d04b-81df-4a34-a3a0-e041f6075221/GCF_008153345.1_ASM815334v1_genomic.fna.gz --refList GCF_008153345.1_ASM815334v1_genomic.fna/target_genomes.txt --output GCF_008153345.1_ASM815334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:20,122] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:20,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:20,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:20,132] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:20,133] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:20,133] [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 phagedenis	strain=B43.1	GCA_008153345.1	162	162	type	True	100.0	1118	1124	95	conclusive
Treponema pedis	strain=T3552B	GCA_017161325.1	409322	409322	type	True	77.2806	67	1124	95	below_threshold
Treponema putidum	strain=OMZ 758	GCA_000755145.1	221027	221027	type	True	76.9619	68	1124	95	below_threshold
Treponema denticola	strain=ATCC 35405	GCA_000008185.1	158	158	type	True	76.6859	64	1124	95	below_threshold
Treponema putidum	strain=ATCC 700334	GCA_007830595.1	221027	221027	type	True	76.5221	64	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,134] [INFO] DFAST Taxonomy check result was written to GCF_008153345.1_ASM815334v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:20,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:20,135] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:20,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference/checkm_data
[2024-01-24 13:46:20,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:20,169] [INFO] Task started: CheckM
[2024-01-24 13:46:20,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008153345.1_ASM815334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008153345.1_ASM815334v1_genomic.fna/checkm_input GCF_008153345.1_ASM815334v1_genomic.fna/checkm_result
[2024-01-24 13:46:48,527] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:48,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:48,546] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:48,546] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:48,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008153345.1_ASM815334v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:48,547] [INFO] Task started: Blastn
[2024-01-24 13:46:48,548] [INFO] Running command: blastn -query GCF_008153345.1_ASM815334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c912c8e-28dc-4fcf-955c-c0985e47fc17/dqc_reference/reference_markers_gtdb.fasta -out GCF_008153345.1_ASM815334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:49,315] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:49,320] [INFO] Selected 22 target genomes.
[2024-01-24 13:46:49,320] [INFO] Target genome list was writen to GCF_008153345.1_ASM815334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:49,444] [INFO] Task started: fastANI
[2024-01-24 13:46:49,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg49f3d04b-81df-4a34-a3a0-e041f6075221/GCF_008153345.1_ASM815334v1_genomic.fna.gz --refList GCF_008153345.1_ASM815334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008153345.1_ASM815334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:02,024] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:02,031] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:02,031] [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_008153345.1	s__Treponema phagedenis	100.0	1118	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	99.50	99.07	0.94	0.88	14	conclusive
GCF_017161325.1	s__Treponema_B pedis	77.1109	66	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	98.52	98.29	0.95	0.86	7	-
GCF_018336815.1	s__Treponema sp018336815	77.1102	67	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775995.1	s__Treponema sp000775995	76.9989	63	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000755145.1	s__Treponema_B putidum	76.9831	67	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000413095.1	s__Treponema_B denticola_A	76.8559	72	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000008185.1	s__Treponema_B denticola	76.6859	64	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_B	95.0	97.58	96.70	0.92	0.88	17	-
GCF_010365865.1	s__Treponema sp010365865	76.4647	74	1124	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,033] [INFO] GTDB search result was written to GCF_008153345.1_ASM815334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:02,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:02,037] [INFO] DFAST_QC result json was written to GCF_008153345.1_ASM815334v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:02,037] [INFO] DFAST_QC completed!
[2024-01-24 13:47:02,037] [INFO] Total running time: 0h1m3s