[2023-06-30 13:24:11,786] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:11,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:11,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference
[2023-06-30 13:24:13,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:13,073] [INFO] Task started: Prodigal
[2023-06-30 13:24:13,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgccc5ff45-982b-499d-b7c3-7a81536965df/GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:27,431] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:27,431] [INFO] Task started: HMMsearch
[2023-06-30 13:24:27,432] [INFO] Running command: hmmsearch --tblout GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference/reference_markers.hmm GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:27,699] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:27,700] [INFO] Found 6/6 markers.
[2023-06-30 13:24:27,725] [INFO] Query marker FASTA was written to GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 13:24:27,726] [INFO] Task started: Blastn
[2023-06-30 13:24:27,726] [INFO] Running command: blastn -query GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference/reference_markers.fasta -out GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:28,405] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:28,409] [INFO] Selected 36 target genomes.
[2023-06-30 13:24:28,410] [INFO] Target genome list was writen to GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 13:24:28,418] [INFO] Task started: fastANI
[2023-06-30 13:24:28,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgccc5ff45-982b-499d-b7c3-7a81536965df/GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:24:52,504] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:52,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:24:52,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:24:52,520] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:24:52,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:24:52,521] [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
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	76.4294	67	839	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.3765	82	839	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.3566	85	839	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	76.1729	65	839	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	76.1628	63	839	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	76.096	65	839	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	76.0872	53	839	95	below_threshold
Corallococcus interemptor	strain=AB047A	GCA_003668875.1	2316720	2316720	type	True	74.8782	57	839	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	74.8312	56	839	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	74.831	57	839	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.6105	61	839	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:24:52,523] [INFO] DFAST Taxonomy check result was written to GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 13:24:52,523] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:24:52,523] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:24:52,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference/checkm_data
[2023-06-30 13:24:52,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:24:52,551] [INFO] Task started: CheckM
[2023-06-30 13:24:52,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 13:25:33,991] [INFO] Task succeeded: CheckM
[2023-06-30 13:25:33,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:25:34,013] [INFO] ===== Completeness check finished =====
[2023-06-30 13:25:34,013] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:25:34,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 13:25:34,014] [INFO] Task started: Blastn
[2023-06-30 13:25:34,014] [INFO] Running command: blastn -query GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aaa3c0b-1267-49d2-8beb-3299439c0e54/dqc_reference/reference_markers_gtdb.fasta -out GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:25:35,087] [INFO] Task succeeded: Blastn
[2023-06-30 13:25:35,092] [INFO] Selected 18 target genomes.
[2023-06-30 13:25:35,093] [INFO] Target genome list was writen to GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:25:35,103] [INFO] Task started: fastANI
[2023-06-30 13:25:35,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgccc5ff45-982b-499d-b7c3-7a81536965df/GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:25:44,292] [INFO] Task succeeded: fastANI
[2023-06-30 13:25:44,319] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:25:44,319] [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_017477245.1	s__Cryptobacteroides sp017477245	96.844	633	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	conclusive
GCA_017428725.1	s__Cryptobacteroides sp017428725	87.1646	619	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
GCA_017458145.1	s__Cryptobacteroides sp017458145	84.8224	481	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017454905.1	s__Cryptobacteroides sp017454905	84.722	527	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	84.6829	408	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_016290835.1	s__Cryptobacteroides sp016290835	84.612	550	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	84.4604	462	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_902768985.1	s__Cryptobacteroides sp902768985	84.2627	438	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.65	98.07	0.93	0.92	5	-
GCA_902790635.1	s__Cryptobacteroides sp902790635	84.2253	467	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017960585.1	s__Cryptobacteroides sp017960585	84.14	399	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789245.1	s__Cryptobacteroides sp902789245	83.9688	428	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	83.9685	455	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_905234475.1	s__Cryptobacteroides sp905234475	83.8924	434	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	83.4484	232	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235775.1	s__Cryptobacteroides sp905235775	83.3419	349	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744435.1	s__Cryptobacteroides sp012744435	83.3187	415	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	83.2897	378	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548445.1	s__Cryptobacteroides sp017548445	83.2247	338	839	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:25:44,322] [INFO] GTDB search result was written to GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 13:25:44,322] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:25:44,326] [INFO] DFAST_QC result json was written to GCA_946413375.1_SRR12081294_bin.14_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 13:25:44,327] [INFO] DFAST_QC completed!
[2023-06-30 13:25:44,327] [INFO] Total running time: 0h1m33s