[2023-03-14 12:03:55,355] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference
[2023-03-14 12:03:56,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,864] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,864] [INFO] Running command: cat /var/lib/cwl/stgd3a55bc5-60b7-41f5-a5c0-e3edaa9d3b32/OceanDNA-b39606.fa | prodigal -d OceanDNA-b39606/cds.fna -a OceanDNA-b39606/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:05,904] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:05,904] [INFO] Task started: HMMsearch
[2023-03-14 12:04:05,904] [INFO] Running command: hmmsearch --tblout OceanDNA-b39606/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference/reference_markers.hmm OceanDNA-b39606/protein.faa > /dev/null
[2023-03-14 12:04:06,102] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:06,103] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3a55bc5-60b7-41f5-a5c0-e3edaa9d3b32/OceanDNA-b39606.fa]
[2023-03-14 12:04:06,164] [INFO] Query marker FASTA was written to OceanDNA-b39606/markers.fasta
[2023-03-14 12:04:06,165] [INFO] Task started: Blastn
[2023-03-14 12:04:06,165] [INFO] Running command: blastn -query OceanDNA-b39606/markers.fasta -db /var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference/reference_markers.fasta -out OceanDNA-b39606/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:06,752] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:06,776] [INFO] Selected 27 target genomes.
[2023-03-14 12:04:06,776] [INFO] Target genome list was writen to OceanDNA-b39606/target_genomes.txt
[2023-03-14 12:04:06,793] [INFO] Task started: fastANI
[2023-03-14 12:04:06,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3a55bc5-60b7-41f5-a5c0-e3edaa9d3b32/OceanDNA-b39606.fa --refList OceanDNA-b39606/target_genomes.txt --output OceanDNA-b39606/fastani_result.tsv --threads 1
[2023-03-14 12:04:22,388] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:22,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:22,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:22,388] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:22,388] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:04:22,389] [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
--------------------------------------------------------------------------------
[2023-03-14 12:04:22,395] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39606/tc_result.tsv
[2023-03-14 12:04:22,404] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:22,404] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:22,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference/checkm_data
[2023-03-14 12:04:22,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:22,463] [INFO] Task started: CheckM
[2023-03-14 12:04:22,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39606/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39606/checkm_input OceanDNA-b39606/checkm_result
[2023-03-14 12:04:49,799] [INFO] Task succeeded: CheckM
[2023-03-14 12:04:49,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.74%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:04:49,808] [INFO] ===== Completeness check finished =====
[2023-03-14 12:04:49,808] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:04:49,809] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39606/markers.fasta)
[2023-03-14 12:04:49,810] [INFO] Task started: Blastn
[2023-03-14 12:04:49,810] [INFO] Running command: blastn -query OceanDNA-b39606/markers.fasta -db /var/lib/cwl/stg059d9cbc-78cd-492a-8fa5-18b4834b0e21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39606/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:50,780] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:50,800] [INFO] Selected 13 target genomes.
[2023-03-14 12:04:50,800] [INFO] Target genome list was writen to OceanDNA-b39606/target_genomes_gtdb.txt
[2023-03-14 12:04:50,828] [INFO] Task started: fastANI
[2023-03-14 12:04:50,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3a55bc5-60b7-41f5-a5c0-e3edaa9d3b32/OceanDNA-b39606.fa --refList OceanDNA-b39606/target_genomes_gtdb.txt --output OceanDNA-b39606/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:04:55,752] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:55,759] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:04:55,759] [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_905182245.1	s__HTCC2207 sp905182245	97.7066	302	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002335945.1	s__HTCC2207 sp002335945	93.3235	448	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_905182265.1	s__HTCC2207 sp905182265	79.932	205	528	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	77.9165	114	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.7781	95	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.7539	131	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_000511875.1	s__HTCC2207 sp000511875	77.7366	127	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378645.1	s__HTCC2207 sp002378645	77.6578	136	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_905182855.1	s__HTCC2207 sp905182855	77.5184	109	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.4687	166	528	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	77.2884	159	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:04:55,765] [INFO] GTDB search result was written to OceanDNA-b39606/result_gtdb.tsv
[2023-03-14 12:04:55,774] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:04:55,781] [INFO] DFAST_QC result json was written to OceanDNA-b39606/dqc_result.json
[2023-03-14 12:04:55,781] [INFO] DFAST_QC completed!
[2023-03-14 12:04:55,781] [INFO] Total running time: 0h1m0s