[2023-06-08 01:07:39,338] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:07:39,401] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:07:39,402] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference
[2023-06-08 01:07:40,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:07:40,806] [INFO] Task started: Prodigal
[2023-06-08 01:07:40,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c1778ac-68d3-4bc4-ad37-54457de22277/GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:07:44,836] [INFO] Task succeeded: Prodigal
[2023-06-08 01:07:44,836] [INFO] Task started: HMMsearch
[2023-06-08 01:07:44,837] [INFO] Running command: hmmsearch --tblout GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference/reference_markers.hmm GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:07:45,088] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:07:45,089] [INFO] Found 6/6 markers.
[2023-06-08 01:07:45,113] [INFO] Query marker FASTA was written to GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 01:07:45,113] [INFO] Task started: Blastn
[2023-06-08 01:07:45,113] [INFO] Running command: blastn -query GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference/reference_markers.fasta -out GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:07:45,685] [INFO] Task succeeded: Blastn
[2023-06-08 01:07:45,689] [INFO] Selected 13 target genomes.
[2023-06-08 01:07:45,690] [INFO] Target genome list was writen to GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 01:07:45,691] [INFO] Task started: fastANI
[2023-06-08 01:07:45,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1778ac-68d3-4bc4-ad37-54457de22277/GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:07:53,058] [INFO] Task succeeded: fastANI
[2023-06-08 01:07:53,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:07:53,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:07:53,070] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:07:53,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 01:07:53,070] [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 porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	78.2171	119	636	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	77.1284	82	636	95	below_threshold
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	76.7249	59	636	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.4366	60	636	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	76.2055	66	636	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:07:53,073] [INFO] DFAST Taxonomy check result was written to GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 01:07:53,073] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:07:53,074] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:07:53,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference/checkm_data
[2023-06-08 01:07:53,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:07:53,100] [INFO] Task started: CheckM
[2023-06-08 01:07:53,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 01:08:13,479] [INFO] Task succeeded: CheckM
[2023-06-08 01:08:13,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:08:13,503] [INFO] ===== Completeness check finished =====
[2023-06-08 01:08:13,503] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:08:13,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 01:08:13,504] [INFO] Task started: Blastn
[2023-06-08 01:08:13,504] [INFO] Running command: blastn -query GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e68bbbe-991f-44fd-8e59-8fece426d77d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:08:14,347] [INFO] Task succeeded: Blastn
[2023-06-08 01:08:14,351] [INFO] Selected 19 target genomes.
[2023-06-08 01:08:14,352] [INFO] Target genome list was writen to GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:08:14,358] [INFO] Task started: fastANI
[2023-06-08 01:08:14,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c1778ac-68d3-4bc4-ad37-54457de22277/GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:08:22,542] [INFO] Task succeeded: fastANI
[2023-06-08 01:08:22,564] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:08:22,564] [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_900769985.1	s__Treponema_D sp900769985	98.7183	587	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.33	98.33	0.87	0.87	2	conclusive
GCA_016293495.1	s__Treponema_D sp016293495	78.7341	236	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.53	98.51	0.86	0.85	3	-
GCA_002309195.1	s__Treponema_D sp002309195	78.2088	159	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.61	98.42	0.71	0.58	5	-
GCA_018064525.1	s__Treponema_D sp018064525	78.1686	251	636	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	78.1556	241	636	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_018385415.1	s__Treponema_D sp018385415	78.0812	221	636	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_018066075.1	s__Treponema_D sp018066075	78.0313	174	636	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	77.1869	96	636	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_016297405.1	s__Treponema_D sp016297405	76.6631	50	636	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_014202035.1	s__Treponema_D rectale	76.4366	60	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.45	97.19	0.93	0.91	3	-
GCA_900767955.1	s__Treponema_D sp900767955	76.3194	77	636	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_902772975.1	s__Treponema_D sp902772975	76.2766	108	636	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_900317625.1	s__Treponema_D sp900317625	76.2312	65	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
GCF_000195275.1	s__Treponema_D succinifaciens	76.178	67	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.40	98.24	0.92	0.91	3	-
GCF_014334335.1	s__Treponema_D sp014334335	75.9723	65	636	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 01:08:22,566] [INFO] GTDB search result was written to GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 01:08:22,566] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:08:22,570] [INFO] DFAST_QC result json was written to GCA_945495855.1_SRR7188237_bin.21_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 01:08:22,571] [INFO] DFAST_QC completed!
[2023-06-08 01:08:22,571] [INFO] Total running time: 0h0m43s