[2023-03-18 00:58:44,625] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,625] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,296] [INFO] Running command: cat /var/lib/cwl/stg231b8c8b-4ec8-4826-b595-ee4cee211afe/OceanDNA-b39356.fa | prodigal -d OceanDNA-b39356/cds.fna -a OceanDNA-b39356/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:58:58,026] [INFO] Task succeeded: Prodigal
[2023-03-18 00:58:58,027] [INFO] Task started: HMMsearch
[2023-03-18 00:58:58,027] [INFO] Running command: hmmsearch --tblout OceanDNA-b39356/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference/reference_markers.hmm OceanDNA-b39356/protein.faa > /dev/null
[2023-03-18 00:58:58,218] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:58:58,218] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg231b8c8b-4ec8-4826-b595-ee4cee211afe/OceanDNA-b39356.fa]
[2023-03-18 00:58:58,234] [INFO] Query marker FASTA was written to OceanDNA-b39356/markers.fasta
[2023-03-18 00:58:58,235] [INFO] Task started: Blastn
[2023-03-18 00:58:58,235] [INFO] Running command: blastn -query OceanDNA-b39356/markers.fasta -db /var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference/reference_markers.fasta -out OceanDNA-b39356/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:58:58,857] [INFO] Task succeeded: Blastn
[2023-03-18 00:58:58,859] [INFO] Selected 28 target genomes.
[2023-03-18 00:58:58,860] [INFO] Target genome list was writen to OceanDNA-b39356/target_genomes.txt
[2023-03-18 00:58:58,873] [INFO] Task started: fastANI
[2023-03-18 00:58:58,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg231b8c8b-4ec8-4826-b595-ee4cee211afe/OceanDNA-b39356.fa --refList OceanDNA-b39356/target_genomes.txt --output OceanDNA-b39356/fastani_result.tsv --threads 1
[2023-03-18 00:59:14,695] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:14,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:14,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:14,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:14,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:59:14,696] [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
--------------------------------------------------------------------------------
[2023-03-18 00:59:14,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39356/tc_result.tsv
[2023-03-18 00:59:14,698] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:14,698] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:14,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference/checkm_data
[2023-03-18 00:59:14,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:14,726] [INFO] Task started: CheckM
[2023-03-18 00:59:14,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39356/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39356/checkm_input OceanDNA-b39356/checkm_result
[2023-03-18 00:59:47,193] [INFO] Task succeeded: CheckM
[2023-03-18 00:59:47,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.43%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:59:47,196] [INFO] ===== Completeness check finished =====
[2023-03-18 00:59:47,196] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:59:47,197] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39356/markers.fasta)
[2023-03-18 00:59:47,197] [INFO] Task started: Blastn
[2023-03-18 00:59:47,197] [INFO] Running command: blastn -query OceanDNA-b39356/markers.fasta -db /var/lib/cwl/stg77ab0d54-bff0-4828-8260-6f31e6cd260c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39356/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:48,239] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:48,240] [INFO] Selected 10 target genomes.
[2023-03-18 00:59:48,240] [INFO] Target genome list was writen to OceanDNA-b39356/target_genomes_gtdb.txt
[2023-03-18 00:59:48,253] [INFO] Task started: fastANI
[2023-03-18 00:59:48,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg231b8c8b-4ec8-4826-b595-ee4cee211afe/OceanDNA-b39356.fa --refList OceanDNA-b39356/target_genomes_gtdb.txt --output OceanDNA-b39356/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:59:52,752] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:52,758] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:59:52,758] [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_017858295.1	s__HTCC2207 sp017858295	94.8928	411	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_000511875.1	s__HTCC2207 sp000511875	85.83	586	649	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	85.028	378	649	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	84.9107	562	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_905478975.1	s__HTCC2207 sp905478975	84.2844	426	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858135.1	s__HTCC2207 sp017858135	80.2608	377	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_018607545.1	s__HTCC2207 sp018607545	78.4675	109	649	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	77.6969	157	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_018664075.1	s__HTCC2207 sp018664075	77.6173	136	649	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	77.4621	147	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:59:52,759] [INFO] GTDB search result was written to OceanDNA-b39356/result_gtdb.tsv
[2023-03-18 00:59:52,759] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:59:52,761] [INFO] DFAST_QC result json was written to OceanDNA-b39356/dqc_result.json
[2023-03-18 00:59:52,761] [INFO] DFAST_QC completed!
[2023-03-18 00:59:52,761] [INFO] Total running time: 0h1m8s