[2023-06-17 07:31:07,199] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:31:07,202] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:31:07,202] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference
[2023-06-17 07:31:09,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:31:09,034] [INFO] Task started: Prodigal
[2023-06-17 07:31:09,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b2f51ca-3eb6-4be5-8c44-d5cfb1c5f5a4/GCA_028719965.1_ASM2871996v1_genomic.fna.gz | prodigal -d GCA_028719965.1_ASM2871996v1_genomic.fna/cds.fna -a GCA_028719965.1_ASM2871996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:31:14,089] [INFO] Task succeeded: Prodigal
[2023-06-17 07:31:14,090] [INFO] Task started: HMMsearch
[2023-06-17 07:31:14,090] [INFO] Running command: hmmsearch --tblout GCA_028719965.1_ASM2871996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference/reference_markers.hmm GCA_028719965.1_ASM2871996v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:31:14,340] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:31:14,341] [INFO] Found 6/6 markers.
[2023-06-17 07:31:14,368] [INFO] Query marker FASTA was written to GCA_028719965.1_ASM2871996v1_genomic.fna/markers.fasta
[2023-06-17 07:31:14,369] [INFO] Task started: Blastn
[2023-06-17 07:31:14,369] [INFO] Running command: blastn -query GCA_028719965.1_ASM2871996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference/reference_markers.fasta -out GCA_028719965.1_ASM2871996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:31:14,918] [INFO] Task succeeded: Blastn
[2023-06-17 07:31:14,923] [INFO] Selected 16 target genomes.
[2023-06-17 07:31:14,923] [INFO] Target genome list was writen to GCA_028719965.1_ASM2871996v1_genomic.fna/target_genomes.txt
[2023-06-17 07:31:14,928] [INFO] Task started: fastANI
[2023-06-17 07:31:14,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b2f51ca-3eb6-4be5-8c44-d5cfb1c5f5a4/GCA_028719965.1_ASM2871996v1_genomic.fna.gz --refList GCA_028719965.1_ASM2871996v1_genomic.fna/target_genomes.txt --output GCA_028719965.1_ASM2871996v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:31:22,268] [INFO] Task succeeded: fastANI
[2023-06-17 07:31:22,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:31:22,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:31:22,281] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 07:31:22,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 07:31:22,282] [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	98.8461	711	743	95	conclusive
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	79.5272	115	743	95	below_threshold
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	78.7783	171	743	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	77.3367	96	743	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	76.9131	89	743	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:31:22,300] [INFO] DFAST Taxonomy check result was written to GCA_028719965.1_ASM2871996v1_genomic.fna/tc_result.tsv
[2023-06-17 07:31:22,301] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:31:22,301] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:31:22,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference/checkm_data
[2023-06-17 07:31:22,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:31:22,345] [INFO] Task started: CheckM
[2023-06-17 07:31:22,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028719965.1_ASM2871996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028719965.1_ASM2871996v1_genomic.fna/checkm_input GCA_028719965.1_ASM2871996v1_genomic.fna/checkm_result
[2023-06-17 07:31:44,307] [INFO] Task succeeded: CheckM
[2023-06-17 07:31:44,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:31:44,331] [INFO] ===== Completeness check finished =====
[2023-06-17 07:31:44,332] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:31:44,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028719965.1_ASM2871996v1_genomic.fna/markers.fasta)
[2023-06-17 07:31:44,333] [INFO] Task started: Blastn
[2023-06-17 07:31:44,333] [INFO] Running command: blastn -query GCA_028719965.1_ASM2871996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ecb55a1-a0f4-4a11-ad5a-173a6065ed0d/dqc_reference/reference_markers_gtdb.fasta -out GCA_028719965.1_ASM2871996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:31:45,080] [INFO] Task succeeded: Blastn
[2023-06-17 07:31:45,085] [INFO] Selected 20 target genomes.
[2023-06-17 07:31:45,085] [INFO] Target genome list was writen to GCA_028719965.1_ASM2871996v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:31:45,090] [INFO] Task started: fastANI
[2023-06-17 07:31:45,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b2f51ca-3eb6-4be5-8c44-d5cfb1c5f5a4/GCA_028719965.1_ASM2871996v1_genomic.fna.gz --refList GCA_028719965.1_ASM2871996v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028719965.1_ASM2871996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:31:53,811] [INFO] Task succeeded: fastANI
[2023-06-17 07:31:53,830] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:31:53,831] [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_000195275.1	s__Treponema_D succinifaciens	98.8461	711	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.40	98.24	0.92	0.91	3	conclusive
GCA_002449305.1	s__Treponema_D sp002449305	91.8128	595	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.77	97.10	0.90	0.86	10	-
GCF_900167025.1	s__Treponema_D berlinense	79.5272	115	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.85	98.81	0.93	0.90	4	-
GCF_016117655.1	s__Treponema_D sp900541995	78.8386	172	743	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_018385315.1	s__Treponema_D sp018385315	78.0721	52	743	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_017935745.1	s__Treponema_D sp017935745	77.5985	232	743	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_016294035.1	s__Treponema_D sp016294035	77.3283	126	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.69	98.66	0.93	0.91	3	-
GCA_002477955.1	s__Treponema_D sp002477955	77.2644	102	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.57	99.37	0.91	0.86	7	-
GCA_016293645.1	s__Treponema_D sp016293645	77.0849	109	743	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_902766345.1	s__Treponema_D sp902766345	76.8597	58	743	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_016296655.1	s__Treponema_D sp016296655	76.6062	82	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421345.1	s__Treponema_D bryantii_B	76.5916	54	743	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	76.557	67	743	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_017553635.1	s__Treponema_D sp017553635	76.5253	58	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.74	98.74	0.94	0.94	2	-
GCA_900767955.1	s__Treponema_D sp900767955	75.9787	55	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.06	96.06	0.87	0.77	5	-
GCA_016282455.1	s__Treponema_D sp016282455	75.7642	56	743	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 07:31:53,833] [INFO] GTDB search result was written to GCA_028719965.1_ASM2871996v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:31:53,834] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:31:53,837] [INFO] DFAST_QC result json was written to GCA_028719965.1_ASM2871996v1_genomic.fna/dqc_result.json
[2023-06-17 07:31:53,838] [INFO] DFAST_QC completed!
[2023-06-17 07:31:53,838] [INFO] Total running time: 0h0m47s