[2024-01-24 12:40:06,735] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:06,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:06,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference
[2024-01-24 12:40:08,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,023] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg775f45aa-15fe-4cf7-aa1b-2890d9855046/GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna.gz | prodigal -d GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/cds.fna -a GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:14,553] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:14,553] [INFO] Task started: HMMsearch
[2024-01-24 12:40:14,553] [INFO] Running command: hmmsearch --tblout GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference/reference_markers.hmm GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:14,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:14,725] [INFO] Found 6/6 markers.
[2024-01-24 12:40:14,751] [INFO] Query marker FASTA was written to GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/markers.fasta
[2024-01-24 12:40:14,752] [INFO] Task started: Blastn
[2024-01-24 12:40:14,752] [INFO] Running command: blastn -query GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference/reference_markers.fasta -out GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:15,299] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:15,302] [INFO] Selected 11 target genomes.
[2024-01-24 12:40:15,302] [INFO] Target genome list was writen to GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:15,307] [INFO] Task started: fastANI
[2024-01-24 12:40:15,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg775f45aa-15fe-4cf7-aa1b-2890d9855046/GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna.gz --refList GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/target_genomes.txt --output GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:22,474] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:22,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:22,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:22,494] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:22,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:22,494] [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 medium	strain=ATCC 700293	GCA_000413035.1	58231	58231	type	True	99.9999	907	909	95	conclusive
Treponema medium	strain=ATCC 700293	GCA_017161265.1	58231	58231	type	True	99.9776	906	909	95	conclusive
Treponema putidum	strain=OMZ 758	GCA_000755145.1	221027	221027	type	True	80.9815	109	909	95	below_threshold
Treponema putidum	strain=ATCC 700334	GCA_007830595.1	221027	221027	type	True	80.8225	108	909	95	below_threshold
Treponema denticola	strain=ATCC 35405	GCA_000008185.1	158	158	type	True	80.7009	112	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:22,495] [INFO] DFAST Taxonomy check result was written to GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:22,496] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:22,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:22,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference/checkm_data
[2024-01-24 12:40:22,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:22,524] [INFO] Task started: CheckM
[2024-01-24 12:40:22,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/checkm_input GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/checkm_result
[2024-01-24 12:40:46,707] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:46,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:46,728] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:46,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:46,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/markers.fasta)
[2024-01-24 12:40:46,729] [INFO] Task started: Blastn
[2024-01-24 12:40:46,729] [INFO] Running command: blastn -query GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad2a352-416e-4d26-886c-ed61f6206713/dqc_reference/reference_markers_gtdb.fasta -out GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:47,579] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:47,582] [INFO] Selected 7 target genomes.
[2024-01-24 12:40:47,582] [INFO] Target genome list was writen to GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:47,601] [INFO] Task started: fastANI
[2024-01-24 12:40:47,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg775f45aa-15fe-4cf7-aa1b-2890d9855046/GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna.gz --refList GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:54,431] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:54,438] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:54,438] [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_017161265.1	s__Treponema medium	99.9776	907	909	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	98.62	97.26	0.99	0.99	3	conclusive
GCF_018336815.1	s__Treponema sp018336815	91.5786	725	909	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	90.7727	701	909	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365865.1	s__Treponema sp010365865	90.161	715	909	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373565.1	s__Treponema sp905373565	88.0188	469	909	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412995.1	s__Treponema vincentii	85.0747	624	909	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema	95.0	97.95	97.95	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,439] [INFO] GTDB search result was written to GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:54,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:54,442] [INFO] DFAST_QC result json was written to GCF_000413035.1_Trep_medi_ATCC_700293_V1_genomic.fna/dqc_result.json
[2024-01-24 12:40:54,443] [INFO] DFAST_QC completed!
[2024-01-24 12:40:54,443] [INFO] Total running time: 0h0m48s