[2023-06-26 22:57:04,551] [INFO] DFAST_QC pipeline started.
[2023-06-26 22:57:04,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 22:57:04,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference
[2023-06-26 22:57:05,702] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 22:57:05,703] [INFO] Task started: Prodigal
[2023-06-26 22:57:05,703] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0ede175-eec1-4cef-91fc-1a408259f203/GCA_002476565.1_ASM247656v1_genomic.fna.gz | prodigal -d GCA_002476565.1_ASM247656v1_genomic.fna/cds.fna -a GCA_002476565.1_ASM247656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 22:57:09,750] [INFO] Task succeeded: Prodigal
[2023-06-26 22:57:09,750] [INFO] Task started: HMMsearch
[2023-06-26 22:57:09,750] [INFO] Running command: hmmsearch --tblout GCA_002476565.1_ASM247656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference/reference_markers.hmm GCA_002476565.1_ASM247656v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 22:57:09,923] [INFO] Task succeeded: HMMsearch
[2023-06-26 22:57:09,924] [INFO] Found 6/6 markers.
[2023-06-26 22:57:09,966] [INFO] Query marker FASTA was written to GCA_002476565.1_ASM247656v1_genomic.fna/markers.fasta
[2023-06-26 22:57:09,967] [INFO] Task started: Blastn
[2023-06-26 22:57:09,967] [INFO] Running command: blastn -query GCA_002476565.1_ASM247656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference/reference_markers.fasta -out GCA_002476565.1_ASM247656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:57:10,517] [INFO] Task succeeded: Blastn
[2023-06-26 22:57:10,521] [INFO] Selected 13 target genomes.
[2023-06-26 22:57:10,521] [INFO] Target genome list was writen to GCA_002476565.1_ASM247656v1_genomic.fna/target_genomes.txt
[2023-06-26 22:57:10,524] [INFO] Task started: fastANI
[2023-06-26 22:57:10,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0ede175-eec1-4cef-91fc-1a408259f203/GCA_002476565.1_ASM247656v1_genomic.fna.gz --refList GCA_002476565.1_ASM247656v1_genomic.fna/target_genomes.txt --output GCA_002476565.1_ASM247656v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 22:57:16,546] [INFO] Task succeeded: fastANI
[2023-06-26 22:57:16,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 22:57:16,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 22:57:16,552] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 22:57:16,552] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 22:57:16,552] [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 succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	80.5931	124	653	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	77.4244	93	653	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 22:57:16,554] [INFO] DFAST Taxonomy check result was written to GCA_002476565.1_ASM247656v1_genomic.fna/tc_result.tsv
[2023-06-26 22:57:16,555] [INFO] ===== Taxonomy check completed =====
[2023-06-26 22:57:16,555] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 22:57:16,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference/checkm_data
[2023-06-26 22:57:16,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 22:57:16,611] [INFO] Task started: CheckM
[2023-06-26 22:57:16,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002476565.1_ASM247656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002476565.1_ASM247656v1_genomic.fna/checkm_input GCA_002476565.1_ASM247656v1_genomic.fna/checkm_result
[2023-06-26 22:57:35,421] [INFO] Task succeeded: CheckM
[2023-06-26 22:57:35,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 22:57:35,443] [INFO] ===== Completeness check finished =====
[2023-06-26 22:57:35,443] [INFO] ===== Start GTDB Search =====
[2023-06-26 22:57:35,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002476565.1_ASM247656v1_genomic.fna/markers.fasta)
[2023-06-26 22:57:35,444] [INFO] Task started: Blastn
[2023-06-26 22:57:35,444] [INFO] Running command: blastn -query GCA_002476565.1_ASM247656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6498e7cf-36a1-4e06-b1dd-2bc84357ee3b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002476565.1_ASM247656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:57:36,183] [INFO] Task succeeded: Blastn
[2023-06-26 22:57:36,187] [INFO] Selected 17 target genomes.
[2023-06-26 22:57:36,187] [INFO] Target genome list was writen to GCA_002476565.1_ASM247656v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 22:57:36,223] [INFO] Task started: fastANI
[2023-06-26 22:57:36,223] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0ede175-eec1-4cef-91fc-1a408259f203/GCA_002476565.1_ASM247656v1_genomic.fna.gz --refList GCA_002476565.1_ASM247656v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002476565.1_ASM247656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 22:57:43,516] [INFO] Task succeeded: fastANI
[2023-06-26 22:57:43,527] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 22:57:43,528] [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_002437725.1	s__Treponema_D sp002437725	98.9303	584	653	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.48	98.76	0.93	0.84	13	conclusive
GCA_002478955.1	s__Treponema_D sp002478955	83.8441	165	653	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_900541945.1	s__Treponema_D sp900541945	79.8571	160	653	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_900317625.1	s__Treponema_D sp900317625	79.4729	153	653	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_017381365.1	s__Treponema_D sp017381365	77.6292	97	653	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.14	97.14	0.75	0.75	2	-
GCF_900167145.1	s__Treponema_D porcinum	77.4563	92	653	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_017386165.1	s__Treponema_D sp017386165	77.2495	87	653	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_902797305.1	s__Treponema_D sp902797305	77.1951	78	653	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_900769975.1	s__Treponema_D sp900769975	77.0897	68	653	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_016293005.1	s__Treponema_D sp016293005	76.8191	80	653	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_017392945.1	s__Treponema_D sp017392945	76.7662	83	653	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_017521105.1	s__Treponema_D sp017521105	76.2068	57	653	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.98	96.98	0.70	0.70	2	-
GCA_002350445.1	s__Treponema_D sp002350445	75.9738	50	653	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.37	99.37	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-26 22:57:43,530] [INFO] GTDB search result was written to GCA_002476565.1_ASM247656v1_genomic.fna/result_gtdb.tsv
[2023-06-26 22:57:43,530] [INFO] ===== GTDB Search completed =====
[2023-06-26 22:57:43,533] [INFO] DFAST_QC result json was written to GCA_002476565.1_ASM247656v1_genomic.fna/dqc_result.json
[2023-06-26 22:57:43,533] [INFO] DFAST_QC completed!
[2023-06-26 22:57:43,533] [INFO] Total running time: 0h0m39s