[2023-06-08 16:15:27,325] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:15:27,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:15:27,328] [INFO] DQC Reference Directory: /var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference
[2023-06-08 16:15:29,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:15:29,844] [INFO] Task started: Prodigal
[2023-06-08 16:15:29,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg153f0543-6b9d-47c6-aa1f-d6924b51489a/GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:15:38,831] [INFO] Task succeeded: Prodigal
[2023-06-08 16:15:38,832] [INFO] Task started: HMMsearch
[2023-06-08 16:15:38,832] [INFO] Running command: hmmsearch --tblout GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference/reference_markers.hmm GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:15:39,123] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:15:39,124] [INFO] Found 6/6 markers.
[2023-06-08 16:15:39,157] [INFO] Query marker FASTA was written to GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 16:15:39,157] [INFO] Task started: Blastn
[2023-06-08 16:15:39,157] [INFO] Running command: blastn -query GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference/reference_markers.fasta -out GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:15:39,731] [INFO] Task succeeded: Blastn
[2023-06-08 16:15:39,735] [INFO] Selected 16 target genomes.
[2023-06-08 16:15:39,736] [INFO] Target genome list was writen to GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 16:15:39,741] [INFO] Task started: fastANI
[2023-06-08 16:15:39,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg153f0543-6b9d-47c6-aa1f-d6924b51489a/GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:15:49,810] [INFO] Task succeeded: fastANI
[2023-06-08 16:15:49,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:15:49,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:15:49,819] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:15:49,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:15:49,819] [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 saccharophilum	strain=DSM 2985	GCA_000255555.2	165	165	type	True	79.5704	367	1109	95	below_threshold
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	78.0125	157	1109	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	76.238	53	1109	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:15:49,821] [INFO] DFAST Taxonomy check result was written to GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 16:15:49,822] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:15:49,822] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:15:49,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference/checkm_data
[2023-06-08 16:15:49,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:15:49,868] [INFO] Task started: CheckM
[2023-06-08 16:15:49,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 16:16:22,810] [INFO] Task succeeded: CheckM
[2023-06-08 16:16:22,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:16:22,838] [INFO] ===== Completeness check finished =====
[2023-06-08 16:16:22,839] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:16:22,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 16:16:22,839] [INFO] Task started: Blastn
[2023-06-08 16:16:22,840] [INFO] Running command: blastn -query GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga370aab1-8ec6-4d5c-be3a-3a5d466e184f/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:16:23,605] [INFO] Task succeeded: Blastn
[2023-06-08 16:16:23,609] [INFO] Selected 20 target genomes.
[2023-06-08 16:16:23,609] [INFO] Target genome list was writen to GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:16:23,625] [INFO] Task started: fastANI
[2023-06-08 16:16:23,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg153f0543-6b9d-47c6-aa1f-d6924b51489a/GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:16:33,586] [INFO] Task succeeded: fastANI
[2023-06-08 16:16:33,608] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 16:16:33,608] [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_017525605.1	s__Treponema_D sp017525605	97.6048	946	1109	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.48	98.48	0.92	0.92	2	conclusive
GCA_017934745.1	s__Treponema_D sp017934745	81.2722	588	1109	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.63	96.63	0.83	0.83	2	-
GCF_000255555.1	s__Treponema_D saccharophilum	79.6117	364	1109	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.00	98.95	0.97	0.97	3	-
GCF_017161305.1	s__Treponema_D ruminis	78.2752	138	1109	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.98	99.98	0.92	0.92	2	-
GCA_902785455.1	s__Treponema_D sp902785455	77.627	128	1109	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_017430385.1	s__Treponema_D sp017430385	77.5495	156	1109	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_017449265.1	s__Treponema_D sp017449265	77.5037	156	1109	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_002404895.1	s__Treponema_D sp002404895	77.1416	155	1109	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_017484285.1	s__Treponema_D sp017484285	77.0164	166	1109	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	76.9898	54	1109	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_017464425.1	s__Treponema_D sp017464425	76.7382	137	1109	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_017450535.1	s__Treponema_D sp017450535	76.0147	63	1109	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 16:16:33,611] [INFO] GTDB search result was written to GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 16:16:33,612] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:16:33,616] [INFO] DFAST_QC result json was written to GCA_947166235.1_SRR8387718_bin.84_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 16:16:33,617] [INFO] DFAST_QC completed!
[2023-06-08 16:16:33,617] [INFO] Total running time: 0h1m6s