[2023-03-19 04:29:37,809] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference
[2023-03-19 04:29:38,905] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,906] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,906] [INFO] Running command: cat /var/lib/cwl/stg0bb06f4f-3681-4144-aa4c-df6b546c004d/OceanDNA-b39392.fa | prodigal -d OceanDNA-b39392/cds.fna -a OceanDNA-b39392/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:51,626] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:51,626] [INFO] Task started: HMMsearch
[2023-03-19 04:29:51,626] [INFO] Running command: hmmsearch --tblout OceanDNA-b39392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference/reference_markers.hmm OceanDNA-b39392/protein.faa > /dev/null
[2023-03-19 04:29:51,809] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:51,809] [INFO] Found 6/6 markers.
[2023-03-19 04:29:51,825] [INFO] Query marker FASTA was written to OceanDNA-b39392/markers.fasta
[2023-03-19 04:29:51,825] [INFO] Task started: Blastn
[2023-03-19 04:29:51,826] [INFO] Running command: blastn -query OceanDNA-b39392/markers.fasta -db /var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference/reference_markers.fasta -out OceanDNA-b39392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:52,457] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:52,458] [INFO] Selected 35 target genomes.
[2023-03-19 04:29:52,458] [INFO] Target genome list was writen to OceanDNA-b39392/target_genomes.txt
[2023-03-19 04:29:52,478] [INFO] Task started: fastANI
[2023-03-19 04:29:52,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb06f4f-3681-4144-aa4c-df6b546c004d/OceanDNA-b39392.fa --refList OceanDNA-b39392/target_genomes.txt --output OceanDNA-b39392/fastani_result.tsv --threads 1
[2023-03-19 04:30:12,128] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:12,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:12,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:12,129] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:12,129] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:30:12,129] [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
--------------------------------------------------------------------------------
[2023-03-19 04:30:12,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39392/tc_result.tsv
[2023-03-19 04:30:12,129] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:12,130] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:12,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference/checkm_data
[2023-03-19 04:30:12,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:12,136] [INFO] Task started: CheckM
[2023-03-19 04:30:12,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39392/checkm_input OceanDNA-b39392/checkm_result
[2023-03-19 04:30:47,439] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:47,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:47,441] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:47,441] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:47,441] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39392/markers.fasta)
[2023-03-19 04:30:47,443] [INFO] Task started: Blastn
[2023-03-19 04:30:47,443] [INFO] Running command: blastn -query OceanDNA-b39392/markers.fasta -db /var/lib/cwl/stg8d25db41-13b4-488f-9c4c-1bad3c2987f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:48,486] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:48,486] [INFO] Selected 10 target genomes.
[2023-03-19 04:30:48,486] [INFO] Target genome list was writen to OceanDNA-b39392/target_genomes_gtdb.txt
[2023-03-19 04:30:48,540] [INFO] Task started: fastANI
[2023-03-19 04:30:48,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bb06f4f-3681-4144-aa4c-df6b546c004d/OceanDNA-b39392.fa --refList OceanDNA-b39392/target_genomes_gtdb.txt --output OceanDNA-b39392/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:52,606] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:52,613] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:30:52,613] [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_017858135.1	s__HTCC2207 sp017858135	98.7478	631	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	conclusive
GCA_905478975.1	s__HTCC2207 sp905478975	79.8877	369	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000511875.1	s__HTCC2207 sp000511875	79.866	406	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478725.1	s__HTCC2207 sp905478725	79.7337	287	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153445.1	s__HTCC2207 sp000153445	79.4562	414	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_017858295.1	s__HTCC2207 sp017858295	79.3145	290	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.293	134	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_018664075.1	s__HTCC2207 sp018664075	77.1098	145	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_018663035.1	s__HTCC2207 sp018663035	76.8676	108	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.8498	101	721	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:52,613] [INFO] GTDB search result was written to OceanDNA-b39392/result_gtdb.tsv
[2023-03-19 04:30:52,613] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:52,614] [INFO] DFAST_QC result json was written to OceanDNA-b39392/dqc_result.json
[2023-03-19 04:30:52,614] [INFO] DFAST_QC completed!
[2023-03-19 04:30:52,614] [INFO] Total running time: 0h1m15s