[2023-03-16 23:35:13,189] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:13,190] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:13,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference
[2023-03-16 23:35:14,953] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,953] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,953] [INFO] Running command: cat /var/lib/cwl/stg6cae48b3-f59b-42cb-8bd5-a6307e8dbcc7/OceanDNA-b34895.fa | prodigal -d OceanDNA-b34895/cds.fna -a OceanDNA-b34895/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:40,109] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:40,110] [INFO] Task started: HMMsearch
[2023-03-16 23:35:40,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b34895/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference/reference_markers.hmm OceanDNA-b34895/protein.faa > /dev/null
[2023-03-16 23:35:40,345] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:40,346] [INFO] Found 6/6 markers.
[2023-03-16 23:35:40,372] [INFO] Query marker FASTA was written to OceanDNA-b34895/markers.fasta
[2023-03-16 23:35:40,373] [INFO] Task started: Blastn
[2023-03-16 23:35:40,373] [INFO] Running command: blastn -query OceanDNA-b34895/markers.fasta -db /var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference/reference_markers.fasta -out OceanDNA-b34895/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:40,992] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:40,992] [INFO] Selected 13 target genomes.
[2023-03-16 23:35:40,993] [INFO] Target genome list was writen to OceanDNA-b34895/target_genomes.txt
[2023-03-16 23:35:41,001] [INFO] Task started: fastANI
[2023-03-16 23:35:41,001] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cae48b3-f59b-42cb-8bd5-a6307e8dbcc7/OceanDNA-b34895.fa --refList OceanDNA-b34895/target_genomes.txt --output OceanDNA-b34895/fastani_result.tsv --threads 1
[2023-03-16 23:35:51,131] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:51,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:51,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:51,137] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:51,137] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:35:51,138] [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
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	83.9815	1011	1507	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	81.0692	843	1507	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	81.0491	834	1507	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	78.2654	263	1507	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.905	285	1507	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	77.6643	159	1507	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.3168	232	1507	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:35:51,138] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34895/tc_result.tsv
[2023-03-16 23:35:51,138] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:51,138] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:51,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference/checkm_data
[2023-03-16 23:35:51,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:51,145] [INFO] Task started: CheckM
[2023-03-16 23:35:51,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34895/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34895/checkm_input OceanDNA-b34895/checkm_result
[2023-03-16 23:36:52,329] [INFO] Task succeeded: CheckM
[2023-03-16 23:36:52,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:36:52,332] [INFO] ===== Completeness check finished =====
[2023-03-16 23:36:52,332] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:36:52,332] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34895/markers.fasta)
[2023-03-16 23:36:52,334] [INFO] Task started: Blastn
[2023-03-16 23:36:52,334] [INFO] Running command: blastn -query OceanDNA-b34895/markers.fasta -db /var/lib/cwl/stg054774bd-4bef-4e93-9764-061d1ce02ebd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34895/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:36:53,317] [INFO] Task succeeded: Blastn
[2023-03-16 23:36:53,362] [INFO] Selected 8 target genomes.
[2023-03-16 23:36:53,362] [INFO] Target genome list was writen to OceanDNA-b34895/target_genomes_gtdb.txt
[2023-03-16 23:36:53,574] [INFO] Task started: fastANI
[2023-03-16 23:36:53,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cae48b3-f59b-42cb-8bd5-a6307e8dbcc7/OceanDNA-b34895.fa --refList OceanDNA-b34895/target_genomes_gtdb.txt --output OceanDNA-b34895/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:37:01,339] [INFO] Task succeeded: fastANI
[2023-03-16 23:37:01,344] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:37:01,344] [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_000314995.1	s__Paraglaciecola arctica	83.9881	1010	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232445.1	s__Paraglaciecola arctica_A	83.5264	468	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	82.1587	913	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	81.0745	842	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCA_905479025.1	s__Paraglaciecola sp905479025	80.3903	394	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	79.7222	677	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796765.1	s__Paraglaciecola sp009796765	78.6814	285	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004360155.1	s__Paraglaciecola sp004360155	78.2595	264	1507	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:37:01,344] [INFO] GTDB search result was written to OceanDNA-b34895/result_gtdb.tsv
[2023-03-16 23:37:01,345] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:37:01,346] [INFO] DFAST_QC result json was written to OceanDNA-b34895/dqc_result.json
[2023-03-16 23:37:01,346] [INFO] DFAST_QC completed!
[2023-03-16 23:37:01,346] [INFO] Total running time: 0h1m48s