[2023-03-15 23:52:16,455] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:52:16,455] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:52:16,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference
[2023-03-15 23:52:17,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:52:17,607] [INFO] Task started: Prodigal
[2023-03-15 23:52:17,607] [INFO] Running command: cat /var/lib/cwl/stgf49d6507-9c55-42ab-9d37-f7896473d0ce/OceanDNA-b39545.fa | prodigal -d OceanDNA-b39545/cds.fna -a OceanDNA-b39545/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:52:32,111] [INFO] Task succeeded: Prodigal
[2023-03-15 23:52:32,112] [INFO] Task started: HMMsearch
[2023-03-15 23:52:32,112] [INFO] Running command: hmmsearch --tblout OceanDNA-b39545/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference/reference_markers.hmm OceanDNA-b39545/protein.faa > /dev/null
[2023-03-15 23:52:32,307] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:52:32,307] [INFO] Found 6/6 markers.
[2023-03-15 23:52:32,322] [INFO] Query marker FASTA was written to OceanDNA-b39545/markers.fasta
[2023-03-15 23:52:32,323] [INFO] Task started: Blastn
[2023-03-15 23:52:32,323] [INFO] Running command: blastn -query OceanDNA-b39545/markers.fasta -db /var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference/reference_markers.fasta -out OceanDNA-b39545/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:52:32,939] [INFO] Task succeeded: Blastn
[2023-03-15 23:52:32,940] [INFO] Selected 35 target genomes.
[2023-03-15 23:52:32,940] [INFO] Target genome list was writen to OceanDNA-b39545/target_genomes.txt
[2023-03-15 23:52:33,082] [INFO] Task started: fastANI
[2023-03-15 23:52:33,082] [INFO] Running command: fastANI --query /var/lib/cwl/stgf49d6507-9c55-42ab-9d37-f7896473d0ce/OceanDNA-b39545.fa --refList OceanDNA-b39545/target_genomes.txt --output OceanDNA-b39545/fastani_result.tsv --threads 1
[2023-03-15 23:52:57,875] [INFO] Task succeeded: fastANI
[2023-03-15 23:52:57,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:52:57,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:52:57,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:52:57,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:52:57,876] [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
--------------------------------------------------------------------------------
[2023-03-15 23:52:57,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39545/tc_result.tsv
[2023-03-15 23:52:57,876] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:52:57,876] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:52:57,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference/checkm_data
[2023-03-15 23:52:57,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:52:57,884] [INFO] Task started: CheckM
[2023-03-15 23:52:57,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39545/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39545/checkm_input OceanDNA-b39545/checkm_result
[2023-03-15 23:53:38,843] [INFO] Task succeeded: CheckM
[2023-03-15 23:53:38,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:53:38,847] [INFO] ===== Completeness check finished =====
[2023-03-15 23:53:38,847] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:53:38,847] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39545/markers.fasta)
[2023-03-15 23:53:38,849] [INFO] Task started: Blastn
[2023-03-15 23:53:38,849] [INFO] Running command: blastn -query OceanDNA-b39545/markers.fasta -db /var/lib/cwl/stg4e11e975-fcb8-4717-af1c-fe7823df3fe3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39545/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:53:40,027] [INFO] Task succeeded: Blastn
[2023-03-15 23:53:40,029] [INFO] Selected 18 target genomes.
[2023-03-15 23:53:40,029] [INFO] Target genome list was writen to OceanDNA-b39545/target_genomes_gtdb.txt
[2023-03-15 23:53:40,159] [INFO] Task started: fastANI
[2023-03-15 23:53:40,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgf49d6507-9c55-42ab-9d37-f7896473d0ce/OceanDNA-b39545.fa --refList OceanDNA-b39545/target_genomes_gtdb.txt --output OceanDNA-b39545/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:53:48,212] [INFO] Task succeeded: fastANI
[2023-03-15 23:53:48,221] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:53:48,221] [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_002334915.1	s__HTCC2207 sp002334915	85.7259	531	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_002378645.1	s__HTCC2207 sp002378645	83.2527	553	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_018664075.1	s__HTCC2207 sp018664075	80.8415	339	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.7032	319	824	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	78.5067	281	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_002335945.1	s__HTCC2207 sp002335945	78.1076	208	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_905182245.1	s__HTCC2207 sp905182245	77.6962	132	824	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	77.6107	186	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381985.1	s__HTCC2207 sp014381985	77.4773	80	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	96.01	96.01	0.94	0.94	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.4434	195	824	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	77.0655	168	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182855.1	s__HTCC2207 sp905182855	76.9632	109	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607545.1	s__HTCC2207 sp018607545	76.9293	66	824	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	76.8281	136	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_004535795.1	s__LSUCC0057 sp004535795	76.3513	50	824	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__LSUCC0057	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:53:48,222] [INFO] GTDB search result was written to OceanDNA-b39545/result_gtdb.tsv
[2023-03-15 23:53:48,222] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:53:48,223] [INFO] DFAST_QC result json was written to OceanDNA-b39545/dqc_result.json
[2023-03-15 23:53:48,223] [INFO] DFAST_QC completed!
[2023-03-15 23:53:48,223] [INFO] Total running time: 0h1m32s