[2023-06-19 02:03:19,493] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:03:19,495] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:03:19,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference
[2023-06-19 02:03:20,874] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:03:20,875] [INFO] Task started: Prodigal
[2023-06-19 02:03:20,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg802baaa3-4029-4923-b29b-7d36f9e4d15c/GCA_014803585.1_ASM1480358v1_genomic.fna.gz | prodigal -d GCA_014803585.1_ASM1480358v1_genomic.fna/cds.fna -a GCA_014803585.1_ASM1480358v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:03:26,495] [INFO] Task succeeded: Prodigal
[2023-06-19 02:03:26,496] [INFO] Task started: HMMsearch
[2023-06-19 02:03:26,496] [INFO] Running command: hmmsearch --tblout GCA_014803585.1_ASM1480358v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference/reference_markers.hmm GCA_014803585.1_ASM1480358v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:03:26,740] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:03:26,741] [INFO] Found 6/6 markers.
[2023-06-19 02:03:26,772] [INFO] Query marker FASTA was written to GCA_014803585.1_ASM1480358v1_genomic.fna/markers.fasta
[2023-06-19 02:03:26,772] [INFO] Task started: Blastn
[2023-06-19 02:03:26,772] [INFO] Running command: blastn -query GCA_014803585.1_ASM1480358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference/reference_markers.fasta -out GCA_014803585.1_ASM1480358v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:03:27,388] [INFO] Task succeeded: Blastn
[2023-06-19 02:03:27,392] [INFO] Selected 16 target genomes.
[2023-06-19 02:03:27,392] [INFO] Target genome list was writen to GCA_014803585.1_ASM1480358v1_genomic.fna/target_genomes.txt
[2023-06-19 02:03:27,393] [INFO] Task started: fastANI
[2023-06-19 02:03:27,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg802baaa3-4029-4923-b29b-7d36f9e4d15c/GCA_014803585.1_ASM1480358v1_genomic.fna.gz --refList GCA_014803585.1_ASM1480358v1_genomic.fna/target_genomes.txt --output GCA_014803585.1_ASM1480358v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:03:37,029] [INFO] Task succeeded: fastANI
[2023-06-19 02:03:37,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:03:37,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:03:37,034] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:03:37,034] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:03:37,034] [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	76.1643	59	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:03:37,036] [INFO] DFAST Taxonomy check result was written to GCA_014803585.1_ASM1480358v1_genomic.fna/tc_result.tsv
[2023-06-19 02:03:37,037] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:03:37,037] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:03:37,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference/checkm_data
[2023-06-19 02:03:37,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:03:37,068] [INFO] Task started: CheckM
[2023-06-19 02:03:37,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014803585.1_ASM1480358v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014803585.1_ASM1480358v1_genomic.fna/checkm_input GCA_014803585.1_ASM1480358v1_genomic.fna/checkm_result
[2023-06-19 02:04:02,219] [INFO] Task succeeded: CheckM
[2023-06-19 02:04:02,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:04:02,243] [INFO] ===== Completeness check finished =====
[2023-06-19 02:04:02,243] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:04:02,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014803585.1_ASM1480358v1_genomic.fna/markers.fasta)
[2023-06-19 02:04:02,244] [INFO] Task started: Blastn
[2023-06-19 02:04:02,244] [INFO] Running command: blastn -query GCA_014803585.1_ASM1480358v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaebe49d8-2ed3-410f-a058-8787ffd19f2f/dqc_reference/reference_markers_gtdb.fasta -out GCA_014803585.1_ASM1480358v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:04:03,030] [INFO] Task succeeded: Blastn
[2023-06-19 02:04:03,034] [INFO] Selected 19 target genomes.
[2023-06-19 02:04:03,035] [INFO] Target genome list was writen to GCA_014803585.1_ASM1480358v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:04:03,037] [INFO] Task started: fastANI
[2023-06-19 02:04:03,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg802baaa3-4029-4923-b29b-7d36f9e4d15c/GCA_014803585.1_ASM1480358v1_genomic.fna.gz --refList GCA_014803585.1_ASM1480358v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014803585.1_ASM1480358v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:04:11,705] [INFO] Task succeeded: fastANI
[2023-06-19 02:04:11,713] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:04:11,714] [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_014803985.1	s__Treponema_D sp014803985	98.1141	599	701	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.03	97.81	0.86	0.80	8	conclusive
GCF_900167145.1	s__Treponema_D porcinum	76.1643	59	701	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	-
GCA_900317625.1	s__Treponema_D sp900317625	76.0066	63	701	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-19 02:04:11,716] [INFO] GTDB search result was written to GCA_014803585.1_ASM1480358v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:04:11,717] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:04:11,720] [INFO] DFAST_QC result json was written to GCA_014803585.1_ASM1480358v1_genomic.fna/dqc_result.json
[2023-06-19 02:04:11,720] [INFO] DFAST_QC completed!
[2023-06-19 02:04:11,720] [INFO] Total running time: 0h0m52s