[2023-03-16 06:54:59,093] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:59,094] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:59,094] [INFO] DQC Reference Directory: /var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference
[2023-03-16 06:55:00,183] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,183] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,184] [INFO] Running command: cat /var/lib/cwl/stgbc735989-618c-42c1-bdce-cb3feccde15b/OceanDNA-b39418.fa | prodigal -d OceanDNA-b39418/cds.fna -a OceanDNA-b39418/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:12,199] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:12,200] [INFO] Task started: HMMsearch
[2023-03-16 06:55:12,200] [INFO] Running command: hmmsearch --tblout OceanDNA-b39418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference/reference_markers.hmm OceanDNA-b39418/protein.faa > /dev/null
[2023-03-16 06:55:12,371] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:12,371] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbc735989-618c-42c1-bdce-cb3feccde15b/OceanDNA-b39418.fa]
[2023-03-16 06:55:12,386] [INFO] Query marker FASTA was written to OceanDNA-b39418/markers.fasta
[2023-03-16 06:55:12,388] [INFO] Task started: Blastn
[2023-03-16 06:55:12,388] [INFO] Running command: blastn -query OceanDNA-b39418/markers.fasta -db /var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference/reference_markers.fasta -out OceanDNA-b39418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:12,963] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:12,968] [INFO] Selected 27 target genomes.
[2023-03-16 06:55:12,968] [INFO] Target genome list was writen to OceanDNA-b39418/target_genomes.txt
[2023-03-16 06:55:12,985] [INFO] Task started: fastANI
[2023-03-16 06:55:12,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc735989-618c-42c1-bdce-cb3feccde15b/OceanDNA-b39418.fa --refList OceanDNA-b39418/target_genomes.txt --output OceanDNA-b39418/fastani_result.tsv --threads 1
[2023-03-16 06:55:28,977] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:28,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:55:28,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:55:28,977] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:55:28,977] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:55:28,977] [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
--------------------------------------------------------------------------------
[2023-03-16 06:55:28,980] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39418/tc_result.tsv
[2023-03-16 06:55:28,985] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:55:28,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:28,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference/checkm_data
[2023-03-16 06:55:28,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:28,995] [INFO] Task started: CheckM
[2023-03-16 06:55:28,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39418/checkm_input OceanDNA-b39418/checkm_result
[2023-03-16 06:56:02,613] [INFO] Task succeeded: CheckM
[2023-03-16 06:56:02,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:56:02,702] [INFO] ===== Completeness check finished =====
[2023-03-16 06:56:02,702] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:56:02,703] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39418/markers.fasta)
[2023-03-16 06:56:02,703] [INFO] Task started: Blastn
[2023-03-16 06:56:02,704] [INFO] Running command: blastn -query OceanDNA-b39418/markers.fasta -db /var/lib/cwl/stg14e58197-37f0-4068-8130-3cb79fdbd10f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:03,554] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:03,557] [INFO] Selected 17 target genomes.
[2023-03-16 06:56:03,557] [INFO] Target genome list was writen to OceanDNA-b39418/target_genomes_gtdb.txt
[2023-03-16 06:56:03,597] [INFO] Task started: fastANI
[2023-03-16 06:56:03,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc735989-618c-42c1-bdce-cb3feccde15b/OceanDNA-b39418.fa --refList OceanDNA-b39418/target_genomes_gtdb.txt --output OceanDNA-b39418/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:56:10,853] [INFO] Task succeeded: fastANI
[2023-03-16 06:56:10,860] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:56:10,860] [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_905182855.1	s__HTCC2207 sp905182855	95.753	467	712	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_905182245.1	s__HTCC2207 sp905182245	77.8454	103	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335945.1	s__HTCC2207 sp002335945	77.6575	187	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_905182275.1	s__HTCC2207 sp905182275	77.1522	51	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663035.1	s__HTCC2207 sp018663035	77.0674	87	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	76.8578	117	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685715.1	s__HTCC2207 sp002685715	76.7581	65	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664075.1	s__HTCC2207 sp018664075	76.7067	122	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	76.6301	101	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_017858135.1	s__HTCC2207 sp017858135	76.5387	89	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_001438605.1	s__HTCC2207 sp001438605	76.3107	70	712	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.34	98.71	0.91	0.87	10	-
--------------------------------------------------------------------------------
[2023-03-16 06:56:10,862] [INFO] GTDB search result was written to OceanDNA-b39418/result_gtdb.tsv
[2023-03-16 06:56:10,864] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:56:10,866] [INFO] DFAST_QC result json was written to OceanDNA-b39418/dqc_result.json
[2023-03-16 06:56:10,866] [INFO] DFAST_QC completed!
[2023-03-16 06:56:10,866] [INFO] Total running time: 0h1m12s