[2023-06-27 06:55:07,626] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:55:07,628] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:55:07,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference
[2023-06-27 06:55:08,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:55:08,946] [INFO] Task started: Prodigal
[2023-06-27 06:55:08,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg557a18dd-98f3-4a0d-a173-a7f1dd724d0b/GCA_002297245.1_ASM229724v1_genomic.fna.gz | prodigal -d GCA_002297245.1_ASM229724v1_genomic.fna/cds.fna -a GCA_002297245.1_ASM229724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:55:13,319] [INFO] Task succeeded: Prodigal
[2023-06-27 06:55:13,319] [INFO] Task started: HMMsearch
[2023-06-27 06:55:13,319] [INFO] Running command: hmmsearch --tblout GCA_002297245.1_ASM229724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference/reference_markers.hmm GCA_002297245.1_ASM229724v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:55:13,578] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:55:13,580] [INFO] Found 6/6 markers.
[2023-06-27 06:55:13,632] [INFO] Query marker FASTA was written to GCA_002297245.1_ASM229724v1_genomic.fna/markers.fasta
[2023-06-27 06:55:13,632] [INFO] Task started: Blastn
[2023-06-27 06:55:13,632] [INFO] Running command: blastn -query GCA_002297245.1_ASM229724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference/reference_markers.fasta -out GCA_002297245.1_ASM229724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:55:14,311] [INFO] Task succeeded: Blastn
[2023-06-27 06:55:14,341] [INFO] Selected 11 target genomes.
[2023-06-27 06:55:14,342] [INFO] Target genome list was writen to GCA_002297245.1_ASM229724v1_genomic.fna/target_genomes.txt
[2023-06-27 06:55:14,345] [INFO] Task started: fastANI
[2023-06-27 06:55:14,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg557a18dd-98f3-4a0d-a173-a7f1dd724d0b/GCA_002297245.1_ASM229724v1_genomic.fna.gz --refList GCA_002297245.1_ASM229724v1_genomic.fna/target_genomes.txt --output GCA_002297245.1_ASM229724v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:55:21,641] [INFO] Task succeeded: fastANI
[2023-06-27 06:55:21,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:55:21,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:55:21,647] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:55:21,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:55:21,647] [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	91.7678	542	613	95	below_threshold
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	77.4189	120	613	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	76.2445	67	613	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:55:21,650] [INFO] DFAST Taxonomy check result was written to GCA_002297245.1_ASM229724v1_genomic.fna/tc_result.tsv
[2023-06-27 06:55:21,650] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:55:21,651] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:55:21,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference/checkm_data
[2023-06-27 06:55:21,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:55:21,681] [INFO] Task started: CheckM
[2023-06-27 06:55:21,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002297245.1_ASM229724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002297245.1_ASM229724v1_genomic.fna/checkm_input GCA_002297245.1_ASM229724v1_genomic.fna/checkm_result
[2023-06-27 06:55:43,044] [INFO] Task succeeded: CheckM
[2023-06-27 06:55:43,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:55:43,067] [INFO] ===== Completeness check finished =====
[2023-06-27 06:55:43,067] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:55:43,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002297245.1_ASM229724v1_genomic.fna/markers.fasta)
[2023-06-27 06:55:43,068] [INFO] Task started: Blastn
[2023-06-27 06:55:43,068] [INFO] Running command: blastn -query GCA_002297245.1_ASM229724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826c75aa-0ae7-4c52-a56f-b393b5243016/dqc_reference/reference_markers_gtdb.fasta -out GCA_002297245.1_ASM229724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:55:43,855] [INFO] Task succeeded: Blastn
[2023-06-27 06:55:43,896] [INFO] Selected 19 target genomes.
[2023-06-27 06:55:43,897] [INFO] Target genome list was writen to GCA_002297245.1_ASM229724v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:55:43,928] [INFO] Task started: fastANI
[2023-06-27 06:55:43,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg557a18dd-98f3-4a0d-a173-a7f1dd724d0b/GCA_002297245.1_ASM229724v1_genomic.fna.gz --refList GCA_002297245.1_ASM229724v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002297245.1_ASM229724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:55:52,838] [INFO] Task succeeded: fastANI
[2023-06-27 06:55:52,852] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:55:52,853] [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_002449305.1	s__Treponema_D sp002449305	97.7464	543	613	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.77	97.10	0.90	0.86	10	conclusive
GCF_000195275.1	s__Treponema_D succinifaciens	91.7678	542	613	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.40	98.24	0.92	0.91	3	-
GCA_016294035.1	s__Treponema_D sp016294035	77.6055	92	613	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.69	98.66	0.93	0.91	3	-
GCF_016117655.1	s__Treponema_D sp900541995	77.4424	119	613	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.86	98.78	0.96	0.96	3	-
GCA_017935745.1	s__Treponema_D sp017935745	77.1716	178	613	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_016293645.1	s__Treponema_D sp016293645	76.9973	89	613	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_016287815.1	s__Treponema_D sp016287815	76.4678	59	613	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_902772975.1	s__Treponema_D sp902772975	76.159	59	613	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_900769985.1	s__Treponema_D sp900769985	75.6765	55	613	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.33	98.33	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-27 06:55:52,887] [INFO] GTDB search result was written to GCA_002297245.1_ASM229724v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:55:52,888] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:55:52,899] [INFO] DFAST_QC result json was written to GCA_002297245.1_ASM229724v1_genomic.fna/dqc_result.json
[2023-06-27 06:55:52,899] [INFO] DFAST_QC completed!
[2023-06-27 06:55:52,899] [INFO] Total running time: 0h0m45s