[2023-06-08 15:53:29,706] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:53:29,709] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:53:29,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference
[2023-06-08 15:53:30,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:53:30,975] [INFO] Task started: Prodigal
[2023-06-08 15:53:30,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a582cd7-c430-4540-b7d7-a38df25a1d4c/GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:53:35,118] [INFO] Task succeeded: Prodigal
[2023-06-08 15:53:35,118] [INFO] Task started: HMMsearch
[2023-06-08 15:53:35,118] [INFO] Running command: hmmsearch --tblout GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference/reference_markers.hmm GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:53:35,297] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:53:35,298] [INFO] Found 6/6 markers.
[2023-06-08 15:53:35,319] [INFO] Query marker FASTA was written to GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 15:53:35,319] [INFO] Task started: Blastn
[2023-06-08 15:53:35,319] [INFO] Running command: blastn -query GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference/reference_markers.fasta -out GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:53:35,864] [INFO] Task succeeded: Blastn
[2023-06-08 15:53:35,872] [INFO] Selected 15 target genomes.
[2023-06-08 15:53:35,872] [INFO] Target genome list was writen to GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 15:53:35,874] [INFO] Task started: fastANI
[2023-06-08 15:53:35,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a582cd7-c430-4540-b7d7-a38df25a1d4c/GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:53:40,525] [INFO] Task succeeded: fastANI
[2023-06-08 15:53:40,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:53:40,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:53:40,530] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:53:40,530] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:53:40,530] [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 berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	78.2092	57	568	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:53:40,532] [INFO] DFAST Taxonomy check result was written to GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 15:53:40,533] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:53:40,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:53:40,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference/checkm_data
[2023-06-08 15:53:40,534] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:53:40,559] [INFO] Task started: CheckM
[2023-06-08 15:53:40,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 15:53:59,053] [INFO] Task succeeded: CheckM
[2023-06-08 15:53:59,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:53:59,072] [INFO] ===== Completeness check finished =====
[2023-06-08 15:53:59,072] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:53:59,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 15:53:59,073] [INFO] Task started: Blastn
[2023-06-08 15:53:59,073] [INFO] Running command: blastn -query GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1950c502-02fa-4108-9e64-5cfb6086a952/dqc_reference/reference_markers_gtdb.fasta -out GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:53:59,864] [INFO] Task succeeded: Blastn
[2023-06-08 15:53:59,868] [INFO] Selected 19 target genomes.
[2023-06-08 15:53:59,868] [INFO] Target genome list was writen to GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:53:59,878] [INFO] Task started: fastANI
[2023-06-08 15:53:59,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a582cd7-c430-4540-b7d7-a38df25a1d4c/GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:54:08,274] [INFO] Task succeeded: fastANI
[2023-06-08 15:54:08,289] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 15:54:08,289] [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_900769975.1	s__Treponema_D sp900769975	81.445	286	568	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_018385315.1	s__Treponema_D sp018385315	78.7123	129	568	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_016293915.1	s__Treponema_D sp016293915	78.6191	132	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.46	98.17	0.88	0.85	4	-
GCA_002395155.1	s__Treponema_D sp002395155	78.4097	141	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.78	97.65	0.86	0.82	3	-
GCA_016297805.1	s__Treponema_D sp016297805	78.3188	149	568	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	78.2968	115	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.98	96.98	0.70	0.70	2	-
GCF_900113965.1	s__Treponema_D bryantii_A	78.1794	108	568	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_004554075.1	s__Treponema_D sp004554075	78.1308	110	568	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_902802305.1	s__Treponema_D sp902802305	78.0682	115	568	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_016292805.1	s__Treponema_D sp016292805	78.0395	99	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.76	98.76	0.90	0.90	2	-
GCF_000421345.1	s__Treponema_D bryantii_B	78.0332	102	568	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_016290335.1	s__Treponema_D sp016290335	77.9912	90	568	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_000619925.1	s__Treponema_D sp000619925	77.885	84	568	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_016286535.1	s__Treponema_D sp016286535	77.8345	112	568	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_902789325.1	s__Treponema_D sp902789325	77.6578	117	568	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_015061465.1	s__Treponema_D bryantii_D	77.5375	100	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.46	96.39	0.85	0.81	3	-
GCA_002350445.1	s__Treponema_D sp002350445	77.1048	74	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.37	99.37	0.88	0.88	2	-
GCA_900767955.1	s__Treponema_D sp900767955	76.7532	84	568	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.06	96.06	0.87	0.77	5	-
--------------------------------------------------------------------------------
[2023-06-08 15:54:08,291] [INFO] GTDB search result was written to GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 15:54:08,292] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:54:08,295] [INFO] DFAST_QC result json was written to GCA_945918385.1_SRR11489791_bin.68_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 15:54:08,295] [INFO] DFAST_QC completed!
[2023-06-08 15:54:08,295] [INFO] Total running time: 0h0m39s