[2023-06-08 19:51:11,735] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:51:11,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:51:11,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference
[2023-06-08 19:51:13,771] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:51:13,772] [INFO] Task started: Prodigal
[2023-06-08 19:51:13,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg06958d26-606b-4275-8540-4f380d65ad80/GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:51:19,749] [INFO] Task succeeded: Prodigal
[2023-06-08 19:51:19,750] [INFO] Task started: HMMsearch
[2023-06-08 19:51:19,750] [INFO] Running command: hmmsearch --tblout GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference/reference_markers.hmm GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:51:19,993] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:51:19,994] [INFO] Found 6/6 markers.
[2023-06-08 19:51:20,025] [INFO] Query marker FASTA was written to GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:51:20,025] [INFO] Task started: Blastn
[2023-06-08 19:51:20,026] [INFO] Running command: blastn -query GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference/reference_markers.fasta -out GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:51:20,590] [INFO] Task succeeded: Blastn
[2023-06-08 19:51:20,594] [INFO] Selected 16 target genomes.
[2023-06-08 19:51:20,595] [INFO] Target genome list was writen to GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:51:20,600] [INFO] Task started: fastANI
[2023-06-08 19:51:20,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg06958d26-606b-4275-8540-4f380d65ad80/GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:51:27,742] [INFO] Task succeeded: fastANI
[2023-06-08 19:51:27,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:51:27,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:51:27,755] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:51:27,755] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:51:27,756] [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	82.2342	182	957	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	78.7247	108	957	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	77.5469	92	957	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	77.186	113	957	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:51:27,758] [INFO] DFAST Taxonomy check result was written to GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:51:27,759] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:51:27,759] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:51:27,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference/checkm_data
[2023-06-08 19:51:27,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:51:27,793] [INFO] Task started: CheckM
[2023-06-08 19:51:27,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:51:52,581] [INFO] Task succeeded: CheckM
[2023-06-08 19:51:52,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:51:52,602] [INFO] ===== Completeness check finished =====
[2023-06-08 19:51:52,602] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:51:52,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:51:52,603] [INFO] Task started: Blastn
[2023-06-08 19:51:52,603] [INFO] Running command: blastn -query GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d500a65-9453-4e06-b316-e2ea104c6c84/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:51:53,364] [INFO] Task succeeded: Blastn
[2023-06-08 19:51:53,369] [INFO] Selected 19 target genomes.
[2023-06-08 19:51:53,369] [INFO] Target genome list was writen to GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:51:53,381] [INFO] Task started: fastANI
[2023-06-08 19:51:53,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg06958d26-606b-4275-8540-4f380d65ad80/GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:52:02,408] [INFO] Task succeeded: fastANI
[2023-06-08 19:52:02,441] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:52:02,445] [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_017381365.1	s__Treponema_D sp017381365	98.1239	708	957	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.14	97.14	0.75	0.75	2	conclusive
GCA_017392945.1	s__Treponema_D sp017392945	78.7875	289	957	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_900541945.1	s__Treponema_D sp900541945	78.7651	186	957	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.94	97.90	0.88	0.87	3	-
GCA_016297805.1	s__Treponema_D sp016297805	78.5622	161	957	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	78.4215	154	957	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_017386165.1	s__Treponema_D sp017386165	78.35	189	957	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_900769325.1	s__Treponema_D sp900769325	78.2518	182	957	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	78.2438	192	957	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_000260795.1	s__Treponema_D sp000260795	78.0023	163	957	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_017390125.1	s__Treponema_D sp017390125	77.9486	144	957	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_002478955.1	s__Treponema_D sp002478955	77.8089	185	957	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_902797305.1	s__Treponema_D sp902797305	77.5811	188	957	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_018064905.1	s__Treponema_D sp018064905	77.4138	135	957	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	77.1873	131	957	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	77.1	110	957	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_016283615.1	s__Treponema_D sp016283615	76.9839	89	957	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_014334335.1	s__Treponema_D sp014334335	76.852	78	957	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	76.5579	106	957	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_017622055.1	s__Treponema_D sp017622055	76.5083	85	957	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 19:52:02,470] [INFO] GTDB search result was written to GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:52:02,471] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:52:02,477] [INFO] DFAST_QC result json was written to GCA_945873845.1_SRR17382097_bin.60_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:52:02,477] [INFO] DFAST_QC completed!
[2023-06-08 19:52:02,477] [INFO] Total running time: 0h0m51s