[2023-06-08 11:46:40,499] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:46:40,501] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:46:40,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference
[2023-06-08 11:46:41,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:46:41,725] [INFO] Task started: Prodigal
[2023-06-08 11:46:41,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf72ec18-f19b-4841-90a8-a8cf6a5a0b51/GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:46:46,346] [INFO] Task succeeded: Prodigal
[2023-06-08 11:46:46,346] [INFO] Task started: HMMsearch
[2023-06-08 11:46:46,346] [INFO] Running command: hmmsearch --tblout GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference/reference_markers.hmm GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:46:46,616] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:46:46,617] [INFO] Found 6/6 markers.
[2023-06-08 11:46:46,650] [INFO] Query marker FASTA was written to GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 11:46:46,650] [INFO] Task started: Blastn
[2023-06-08 11:46:46,651] [INFO] Running command: blastn -query GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference/reference_markers.fasta -out GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:46:47,209] [INFO] Task succeeded: Blastn
[2023-06-08 11:46:47,212] [INFO] Selected 17 target genomes.
[2023-06-08 11:46:47,212] [INFO] Target genome list was writen to GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 11:46:47,213] [INFO] Task started: fastANI
[2023-06-08 11:46:47,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf72ec18-f19b-4841-90a8-a8cf6a5a0b51/GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:46:56,766] [INFO] Task succeeded: fastANI
[2023-06-08 11:46:56,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:46:56,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:46:56,777] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:46:56,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:46:56,778] [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	77.7464	75	775	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	77.4646	73	775	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	77.257	62	775	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:46:56,781] [INFO] DFAST Taxonomy check result was written to GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 11:46:56,782] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:46:56,782] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:46:56,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference/checkm_data
[2023-06-08 11:46:56,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:46:56,824] [INFO] Task started: CheckM
[2023-06-08 11:46:56,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 11:47:19,053] [INFO] Task succeeded: CheckM
[2023-06-08 11:47:19,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:47:19,083] [INFO] ===== Completeness check finished =====
[2023-06-08 11:47:19,083] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:47:19,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 11:47:19,084] [INFO] Task started: Blastn
[2023-06-08 11:47:19,084] [INFO] Running command: blastn -query GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f6c7416-4983-4d2d-8071-b8a3778b0682/dqc_reference/reference_markers_gtdb.fasta -out GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:47:19,827] [INFO] Task succeeded: Blastn
[2023-06-08 11:47:19,831] [INFO] Selected 23 target genomes.
[2023-06-08 11:47:19,831] [INFO] Target genome list was writen to GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:47:19,834] [INFO] Task started: fastANI
[2023-06-08 11:47:19,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf72ec18-f19b-4841-90a8-a8cf6a5a0b51/GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:47:30,327] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:30,348] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:47:30,348] [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_016292805.1	s__Treponema_D sp016292805	98.7164	613	775	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.76	98.76	0.90	0.90	2	conclusive
GCA_018385315.1	s__Treponema_D sp018385315	81.6867	288	775	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_016297805.1	s__Treponema_D sp016297805	80.1188	302	775	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	79.5386	310	775	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_002395155.1	s__Treponema_D sp002395155	78.7346	250	775	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_017940255.1	s__Treponema_D sp017940255	78.6374	222	775	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_900113965.1	s__Treponema_D bryantii_A	78.3896	256	775	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	78.3724	241	775	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.46	98.17	0.88	0.85	4	-
GCF_900111035.1	s__Treponema_D bryantii_C	78.2137	251	775	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	78.1752	248	775	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_900769975.1	s__Treponema_D sp900769975	78.0349	193	775	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	77.9093	208	775	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_017962965.1	s__Treponema_D sp017962965	77.7568	164	775	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	77.6884	192	775	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	77.4864	177	775	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.98	96.98	0.70	0.70	2	-
GCA_015061465.1	s__Treponema_D bryantii_D	77.206	136	775	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_900767955.1	s__Treponema_D sp900767955	77.0772	112	775	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_017392945.1	s__Treponema_D sp017392945	77.0481	82	775	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_017936665.1	s__RGIG9060 sp017936665	76.2316	65	775	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__RGIG9060	95.0	97.88	97.76	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-08 11:47:30,350] [INFO] GTDB search result was written to GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 11:47:30,351] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:47:30,355] [INFO] DFAST_QC result json was written to GCA_945495585.1_SRR7188236_bin.26_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 11:47:30,355] [INFO] DFAST_QC completed!
[2023-06-08 11:47:30,355] [INFO] Total running time: 0h0m50s