[2023-06-08 17:47:29,605] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:47:29,607] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:47:29,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference
[2023-06-08 17:47:30,834] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:47:30,835] [INFO] Task started: Prodigal
[2023-06-08 17:47:30,835] [INFO] Running command: gunzip -c /var/lib/cwl/stgf74b5651-f141-4226-8ada-dc12a08927aa/GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:47:35,429] [INFO] Task succeeded: Prodigal
[2023-06-08 17:47:35,429] [INFO] Task started: HMMsearch
[2023-06-08 17:47:35,429] [INFO] Running command: hmmsearch --tblout GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference/reference_markers.hmm GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:47:35,660] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:47:35,662] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf74b5651-f141-4226-8ada-dc12a08927aa/GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna.gz]
[2023-06-08 17:47:35,688] [INFO] Query marker FASTA was written to GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-08 17:47:35,688] [INFO] Task started: Blastn
[2023-06-08 17:47:35,688] [INFO] Running command: blastn -query GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference/reference_markers.fasta -out GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:47:36,368] [INFO] Task succeeded: Blastn
[2023-06-08 17:47:36,372] [INFO] Selected 14 target genomes.
[2023-06-08 17:47:36,372] [INFO] Target genome list was writen to GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-08 17:47:36,374] [INFO] Task started: fastANI
[2023-06-08 17:47:36,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgf74b5651-f141-4226-8ada-dc12a08927aa/GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:47:48,741] [INFO] Task succeeded: fastANI
[2023-06-08 17:47:48,741] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:47:48,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:47:48,753] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-06-08 17:47:48,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 17:47:48,754] [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
Lautropia mirabilis	strain=NCTC12852	GCA_900637555.1	47671	47671	type	True	96.571	401	404	95	conclusive
Lautropia mirabilis	strain=ATCC 51599	GCA_000186425.1	47671	47671	type	True	96.5406	399	404	95	conclusive
Lautropia dentalis	strain=KCOM 2505	GCA_003892345.1	2490857	2490857	type	True	84.3065	346	404	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.2359	112	404	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	77.5564	110	404	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	77.5484	109	404	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.5098	82	404	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	77.4332	85	404	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	77.3898	87	404	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3182	88	404	95	below_threshold
Derxia gummosa	strain=DSM 723	GCA_000482785.1	203699	203699	type	True	77.2522	81	404	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	77.1528	123	404	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.0931	100	404	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.6373	82	404	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:47:48,756] [INFO] DFAST Taxonomy check result was written to GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-08 17:47:48,757] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:47:48,757] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:47:48,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference/checkm_data
[2023-06-08 17:47:48,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:47:48,787] [INFO] Task started: CheckM
[2023-06-08 17:47:48,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-08 17:48:09,687] [INFO] Task succeeded: CheckM
[2023-06-08 17:48:09,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:48:09,707] [INFO] ===== Completeness check finished =====
[2023-06-08 17:48:09,707] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:48:09,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-08 17:48:09,708] [INFO] Task started: Blastn
[2023-06-08 17:48:09,708] [INFO] Running command: blastn -query GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg47637975-a120-4769-bc4c-bf69b6d50fe4/dqc_reference/reference_markers_gtdb.fasta -out GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:48:10,434] [INFO] Task succeeded: Blastn
[2023-06-08 17:48:10,438] [INFO] Selected 12 target genomes.
[2023-06-08 17:48:10,438] [INFO] Target genome list was writen to GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:48:10,445] [INFO] Task started: fastANI
[2023-06-08 17:48:10,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgf74b5651-f141-4226-8ada-dc12a08927aa/GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:48:19,075] [INFO] Task succeeded: fastANI
[2023-06-08 17:48:19,087] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:48:19,088] [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
GCF_900637555.1	s__Lautropia mirabilis	96.571	401	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	97.31	96.25	0.97	0.95	6	conclusive
GCF_003892345.1	s__Lautropia dentalis	84.3351	345	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	98.32	98.32	0.98	0.98	2	-
GCA_018970865.1	s__CAIZPE01 sp018970865	78.7557	97	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898645.1	s__SCN-69-89 sp001898645	78.3083	120	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	99.96	99.96	0.96	0.96	2	-
GCA_012513675.1	s__Lautropia sp012513675	78.1204	85	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379565.1	s__Cupriavidus sp000379565	78.02	103	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813615.1	s__Lautropia sp013813615	77.9126	64	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426345.1	s__Cupriavidus sp000426345	77.5824	96	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.93	98.88	0.87	0.86	3	-
GCA_903898725.1	s__UBA4615 sp903898725	77.5227	100	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	77.5098	82	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261335.1	s__Bordetella sp002261335	77.3577	116	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	98.98	98.98	0.96	0.96	2	-
GCF_013267355.1	s__Achromobacter pestifer_A	77.2159	98	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:48:19,090] [INFO] GTDB search result was written to GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 17:48:19,090] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:48:19,096] [INFO] DFAST_QC result json was written to GCA_927911035.1_ERR3827255_bin.4_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-08 17:48:19,096] [INFO] DFAST_QC completed!
[2023-06-08 17:48:19,096] [INFO] Total running time: 0h0m49s