[2023-06-28 00:28:24,550] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:28:24,552] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:28:24,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference
[2023-06-28 00:28:25,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:28:25,891] [INFO] Task started: Prodigal
[2023-06-28 00:28:25,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg97d99eb3-e8b5-473e-ab87-9399603646fc/GCA_017450845.1_ASM1745084v1_genomic.fna.gz | prodigal -d GCA_017450845.1_ASM1745084v1_genomic.fna/cds.fna -a GCA_017450845.1_ASM1745084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:28:32,858] [INFO] Task succeeded: Prodigal
[2023-06-28 00:28:32,859] [INFO] Task started: HMMsearch
[2023-06-28 00:28:32,859] [INFO] Running command: hmmsearch --tblout GCA_017450845.1_ASM1745084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference/reference_markers.hmm GCA_017450845.1_ASM1745084v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:28:33,112] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:28:33,113] [INFO] Found 6/6 markers.
[2023-06-28 00:28:33,145] [INFO] Query marker FASTA was written to GCA_017450845.1_ASM1745084v1_genomic.fna/markers.fasta
[2023-06-28 00:28:33,146] [INFO] Task started: Blastn
[2023-06-28 00:28:33,146] [INFO] Running command: blastn -query GCA_017450845.1_ASM1745084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference/reference_markers.fasta -out GCA_017450845.1_ASM1745084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:33,780] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:33,784] [INFO] Selected 25 target genomes.
[2023-06-28 00:28:33,785] [INFO] Target genome list was writen to GCA_017450845.1_ASM1745084v1_genomic.fna/target_genomes.txt
[2023-06-28 00:28:33,787] [INFO] Task started: fastANI
[2023-06-28 00:28:33,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d99eb3-e8b5-473e-ab87-9399603646fc/GCA_017450845.1_ASM1745084v1_genomic.fna.gz --refList GCA_017450845.1_ASM1745084v1_genomic.fna/target_genomes.txt --output GCA_017450845.1_ASM1745084v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:28:54,514] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:54,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:28:54,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:28:54,519] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:28:54,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:28:54,519] [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 saccharophilum	strain=DSM 2985	GCA_000255555.2	165	165	type	True	76.1459	75	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:28:54,521] [INFO] DFAST Taxonomy check result was written to GCA_017450845.1_ASM1745084v1_genomic.fna/tc_result.tsv
[2023-06-28 00:28:54,522] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:28:54,522] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:28:54,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference/checkm_data
[2023-06-28 00:28:54,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:28:54,556] [INFO] Task started: CheckM
[2023-06-28 00:28:54,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017450845.1_ASM1745084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017450845.1_ASM1745084v1_genomic.fna/checkm_input GCA_017450845.1_ASM1745084v1_genomic.fna/checkm_result
[2023-06-28 00:29:21,529] [INFO] Task succeeded: CheckM
[2023-06-28 00:29:21,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:29:21,553] [INFO] ===== Completeness check finished =====
[2023-06-28 00:29:21,553] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:29:21,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017450845.1_ASM1745084v1_genomic.fna/markers.fasta)
[2023-06-28 00:29:21,554] [INFO] Task started: Blastn
[2023-06-28 00:29:21,554] [INFO] Running command: blastn -query GCA_017450845.1_ASM1745084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb0f1d8-7da3-4119-88b9-afc709aa0305/dqc_reference/reference_markers_gtdb.fasta -out GCA_017450845.1_ASM1745084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:29:22,500] [INFO] Task succeeded: Blastn
[2023-06-28 00:29:22,504] [INFO] Selected 17 target genomes.
[2023-06-28 00:29:22,504] [INFO] Target genome list was writen to GCA_017450845.1_ASM1745084v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:29:22,514] [INFO] Task started: fastANI
[2023-06-28 00:29:22,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d99eb3-e8b5-473e-ab87-9399603646fc/GCA_017450845.1_ASM1745084v1_genomic.fna.gz --refList GCA_017450845.1_ASM1745084v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017450845.1_ASM1745084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:29:30,391] [INFO] Task succeeded: fastANI
[2023-06-28 00:29:30,399] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:29:30,399] [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_017450845.1	s__Treponema_D sp017450845	100.0	801	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	conclusive
GCA_902773215.1	s__Treponema_D sp902773215	88.4969	457	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_902796985.1	s__Treponema_D sp902796985	87.6633	428	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_017453705.1	s__Treponema_D sp017453705	79.4181	272	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_002393865.1	s__Treponema_D sp002393865	77.2812	144	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.21	0.87	0.87	2	-
GCA_902803415.1	s__Treponema_D sp902803415	76.8473	109	821	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.87	98.87	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-28 00:29:30,402] [INFO] GTDB search result was written to GCA_017450845.1_ASM1745084v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:29:30,402] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:29:30,405] [INFO] DFAST_QC result json was written to GCA_017450845.1_ASM1745084v1_genomic.fna/dqc_result.json
[2023-06-28 00:29:30,405] [INFO] DFAST_QC completed!
[2023-06-28 00:29:30,405] [INFO] Total running time: 0h1m6s