[2023-03-14 13:35:42,284] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:35:42,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:35:42,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference
[2023-03-14 13:35:44,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:35:44,635] [INFO] Task started: Prodigal
[2023-03-14 13:35:44,635] [INFO] Running command: cat /var/lib/cwl/stgeb9557f9-ebeb-4f9d-a132-9d836bbbb368/OceanDNA-b33299.fa | prodigal -d OceanDNA-b33299/cds.fna -a OceanDNA-b33299/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:36:13,459] [INFO] Task succeeded: Prodigal
[2023-03-14 13:36:13,459] [INFO] Task started: HMMsearch
[2023-03-14 13:36:13,459] [INFO] Running command: hmmsearch --tblout OceanDNA-b33299/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference/reference_markers.hmm OceanDNA-b33299/protein.faa > /dev/null
[2023-03-14 13:36:13,703] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:36:13,704] [INFO] Found 6/6 markers.
[2023-03-14 13:36:13,734] [INFO] Query marker FASTA was written to OceanDNA-b33299/markers.fasta
[2023-03-14 13:36:13,735] [INFO] Task started: Blastn
[2023-03-14 13:36:13,735] [INFO] Running command: blastn -query OceanDNA-b33299/markers.fasta -db /var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference/reference_markers.fasta -out OceanDNA-b33299/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:36:14,707] [INFO] Task succeeded: Blastn
[2023-03-14 13:36:14,708] [INFO] Selected 19 target genomes.
[2023-03-14 13:36:14,708] [INFO] Target genome list was writen to OceanDNA-b33299/target_genomes.txt
[2023-03-14 13:36:14,718] [INFO] Task started: fastANI
[2023-03-14 13:36:14,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb9557f9-ebeb-4f9d-a132-9d836bbbb368/OceanDNA-b33299.fa --refList OceanDNA-b33299/target_genomes.txt --output OceanDNA-b33299/fastani_result.tsv --threads 1
[2023-03-14 13:36:37,964] [INFO] Task succeeded: fastANI
[2023-03-14 13:36:37,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:36:37,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:36:37,983] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2023-03-14 13:36:37,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 13:36:37,983] [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
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	98.7438	1320	1397	95	conclusive
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	98.7164	1323	1397	95	conclusive
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	92.9987	1261	1397	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	84.4448	967	1397	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	84.0986	959	1397	95	below_threshold
Cupriavidus neocaledonicus	strain=STM6070	GCA_000372525.1	1040979	1040979	type	True	83.9787	935	1397	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	83.9766	935	1397	95	below_threshold
Cupriavidus lacunae	strain=S23	GCA_003353055.1	2666307	2666307	type	True	83.7284	872	1397	95	below_threshold
Cupriavidus malaysiensis	strain=USMAA1020	GCA_001854325.1	367825	367825	type	True	83.0567	885	1397	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.6343	822	1397	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	79.0446	623	1397	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	79.0424	560	1397	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	78.9575	569	1397	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	78.6509	544	1397	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	78.0345	531	1397	95	below_threshold
Paraburkholderia sediminicola	strain=LMG 24238	GCA_902859805.1	458836	458836	type	True	77.8228	405	1397	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	75.9101	86	1397	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	74.9121	88	1397	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:36:37,983] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33299/tc_result.tsv
[2023-03-14 13:36:37,983] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:36:37,983] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:36:37,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference/checkm_data
[2023-03-14 13:36:37,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:36:38,330] [INFO] Task started: CheckM
[2023-03-14 13:36:38,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33299/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33299/checkm_input OceanDNA-b33299/checkm_result
[2023-03-14 13:38:05,809] [INFO] Task succeeded: CheckM
[2023-03-14 13:38:05,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:38:05,813] [INFO] ===== Completeness check finished =====
[2023-03-14 13:38:05,813] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:38:05,813] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33299/markers.fasta)
[2023-03-14 13:38:05,815] [INFO] Task started: Blastn
[2023-03-14 13:38:05,815] [INFO] Running command: blastn -query OceanDNA-b33299/markers.fasta -db /var/lib/cwl/stgd8b4fa6f-adbc-4672-99a9-5c547e36eb61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33299/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:07,798] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:07,800] [INFO] Selected 15 target genomes.
[2023-03-14 13:38:07,800] [INFO] Target genome list was writen to OceanDNA-b33299/target_genomes_gtdb.txt
[2023-03-14 13:38:07,818] [INFO] Task started: fastANI
[2023-03-14 13:38:07,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb9557f9-ebeb-4f9d-a132-9d836bbbb368/OceanDNA-b33299.fa --refList OceanDNA-b33299/target_genomes_gtdb.txt --output OceanDNA-b33299/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:38:26,865] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:26,875] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:38:26,875] [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_008801915.1	s__Cupriavidus gilardii	98.7438	1320	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.02	95.33	0.92	0.88	7	conclusive
GCF_008632125.1	s__Cupriavidus cauae	92.9987	1261	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.88	98.88	0.93	0.93	2	-
GCF_013314895.1	s__Cupriavidus gilardii_C	92.1222	1236	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.09	95.09	0.91	0.91	2	-
GCF_007829435.1	s__Cupriavidus gilardii_D	84.7581	919	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598055.1	s__Cupriavidus nantongensis	84.1258	956	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.73	95.73	0.81	0.78	3	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	83.977	936	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	83.9662	937	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCF_003353055.1	s__Cupriavidus lacunae	83.7513	869	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.34	96.34	0.71	0.71	2	-
GCF_000876015.1	s__Cupriavidus basilensis_B	83.6967	899	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.55	98.55	0.88	0.88	2	-
GCF_001854325.1	s__Cupriavidus malaysiensis	83.0528	886	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.34	99.30	0.91	0.91	3	-
GCA_003520365.1	s__Massilia sp003520365	78.3462	310	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424165.1	s__Massilia sp001424165	77.9302	394	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403375.1	s__Thiobacillus denitrificans_E	77.7023	221	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013287275.1	s__Undibacterium sp013287275	76.3626	110	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	74.9879	349	1397	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:38:26,875] [INFO] GTDB search result was written to OceanDNA-b33299/result_gtdb.tsv
[2023-03-14 13:38:26,875] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:38:26,877] [INFO] DFAST_QC result json was written to OceanDNA-b33299/dqc_result.json
[2023-03-14 13:38:26,877] [INFO] DFAST_QC completed!
[2023-03-14 13:38:26,877] [INFO] Total running time: 0h2m45s