[2023-03-18 05:53:16,857] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:53:16,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:53:16,857] [INFO] DQC Reference Directory: /var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference
[2023-03-18 05:53:17,976] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:53:17,976] [INFO] Task started: Prodigal
[2023-03-18 05:53:17,976] [INFO] Running command: cat /var/lib/cwl/stgaacd50c7-bb47-4ddb-9c76-57c1e50e2fb2/OceanDNA-b44622.fa | prodigal -d OceanDNA-b44622/cds.fna -a OceanDNA-b44622/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:53:33,047] [INFO] Task succeeded: Prodigal
[2023-03-18 05:53:33,047] [INFO] Task started: HMMsearch
[2023-03-18 05:53:33,047] [INFO] Running command: hmmsearch --tblout OceanDNA-b44622/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference/reference_markers.hmm OceanDNA-b44622/protein.faa > /dev/null
[2023-03-18 05:53:33,225] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:53:33,226] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaacd50c7-bb47-4ddb-9c76-57c1e50e2fb2/OceanDNA-b44622.fa]
[2023-03-18 05:53:33,248] [INFO] Query marker FASTA was written to OceanDNA-b44622/markers.fasta
[2023-03-18 05:53:33,249] [INFO] Task started: Blastn
[2023-03-18 05:53:33,249] [INFO] Running command: blastn -query OceanDNA-b44622/markers.fasta -db /var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference/reference_markers.fasta -out OceanDNA-b44622/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:53:33,794] [INFO] Task succeeded: Blastn
[2023-03-18 05:53:33,795] [INFO] Selected 20 target genomes.
[2023-03-18 05:53:33,795] [INFO] Target genome list was writen to OceanDNA-b44622/target_genomes.txt
[2023-03-18 05:53:33,808] [INFO] Task started: fastANI
[2023-03-18 05:53:33,808] [INFO] Running command: fastANI --query /var/lib/cwl/stgaacd50c7-bb47-4ddb-9c76-57c1e50e2fb2/OceanDNA-b44622.fa --refList OceanDNA-b44622/target_genomes.txt --output OceanDNA-b44622/fastani_result.tsv --threads 1
[2023-03-18 05:53:46,428] [INFO] Task succeeded: fastANI
[2023-03-18 05:53:46,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:53:46,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:53:46,435] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:53:46,435] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:53:46,435] [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
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	75.5629	57	834	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	75.4739	78	834	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	75.3076	63	834	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.2179	63	834	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.1887	65	834	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	75.0724	72	834	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	75.063	77	834	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:53:46,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44622/tc_result.tsv
[2023-03-18 05:53:46,436] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:53:46,436] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:53:46,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference/checkm_data
[2023-03-18 05:53:46,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:53:46,441] [INFO] Task started: CheckM
[2023-03-18 05:53:46,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44622/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44622/checkm_input OceanDNA-b44622/checkm_result
[2023-03-18 05:54:26,229] [INFO] Task succeeded: CheckM
[2023-03-18 05:54:26,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:54:26,398] [INFO] ===== Completeness check finished =====
[2023-03-18 05:54:26,398] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:54:26,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44622/markers.fasta)
[2023-03-18 05:54:26,399] [INFO] Task started: Blastn
[2023-03-18 05:54:26,399] [INFO] Running command: blastn -query OceanDNA-b44622/markers.fasta -db /var/lib/cwl/stga0306986-1a04-4447-9918-e4b346b9b0a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44622/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:54:27,206] [INFO] Task succeeded: Blastn
[2023-03-18 05:54:27,207] [INFO] Selected 18 target genomes.
[2023-03-18 05:54:27,207] [INFO] Target genome list was writen to OceanDNA-b44622/target_genomes_gtdb.txt
[2023-03-18 05:54:27,322] [INFO] Task started: fastANI
[2023-03-18 05:54:27,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgaacd50c7-bb47-4ddb-9c76-57c1e50e2fb2/OceanDNA-b44622.fa --refList OceanDNA-b44622/target_genomes_gtdb.txt --output OceanDNA-b44622/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:54:37,503] [INFO] Task succeeded: fastANI
[2023-03-18 05:54:37,511] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:54:37,511] [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_013042375.1	s__UBA1847 sp013042375	77.173	186	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_009937525.1	s__JAACFE01 sp009937525	77.0773	155	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937505.1	s__JAACFE01 sp009937505	76.808	153	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043165.1	s__UBA1847 sp013043165	76.2959	96	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_009937615.1	s__JAACFB01 sp009937615	76.2545	103	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001045.1	s__UBA1847 sp013001045	76.1778	73	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCA_007693855.1	s__PWYM01 sp007693855	76.1127	70	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PWYM01;f__PWYM01;g__PWYM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054615.1	s__FEN-1219 sp011054615	75.6627	84	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__FEN-1219	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261655.1	s__SG8-30 sp018261655	75.6553	66	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SG8-30	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064545.1	s__XN24 sp011064545	75.5727	56	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202975.1	s__Povalibacter uvarum	75.4739	78	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Povalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	75.3076	63	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293525.1	s__Ideonella_A sakaiensis	75.2511	69	834	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:54:37,512] [INFO] GTDB search result was written to OceanDNA-b44622/result_gtdb.tsv
[2023-03-18 05:54:37,512] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:54:37,514] [INFO] DFAST_QC result json was written to OceanDNA-b44622/dqc_result.json
[2023-03-18 05:54:37,514] [INFO] DFAST_QC completed!
[2023-03-18 05:54:37,514] [INFO] Total running time: 0h1m21s