[2023-03-17 07:44:36,993] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,993] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference
[2023-03-17 07:44:38,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,849] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,850] [INFO] Running command: cat /var/lib/cwl/stg4b34f34d-0ad3-4e07-a7fd-9f1436753740/OceanDNA-b16219.fa | prodigal -d OceanDNA-b16219/cds.fna -a OceanDNA-b16219/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:56,902] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:56,902] [INFO] Task started: HMMsearch
[2023-03-17 07:44:56,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b16219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference/reference_markers.hmm OceanDNA-b16219/protein.faa > /dev/null
[2023-03-17 07:44:57,129] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:57,130] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4b34f34d-0ad3-4e07-a7fd-9f1436753740/OceanDNA-b16219.fa]
[2023-03-17 07:44:57,155] [INFO] Query marker FASTA was written to OceanDNA-b16219/markers.fasta
[2023-03-17 07:44:57,155] [INFO] Task started: Blastn
[2023-03-17 07:44:57,155] [INFO] Running command: blastn -query OceanDNA-b16219/markers.fasta -db /var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference/reference_markers.fasta -out OceanDNA-b16219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:57,678] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:57,678] [INFO] Selected 26 target genomes.
[2023-03-17 07:44:57,679] [INFO] Target genome list was writen to OceanDNA-b16219/target_genomes.txt
[2023-03-17 07:44:57,717] [INFO] Task started: fastANI
[2023-03-17 07:44:57,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b34f34d-0ad3-4e07-a7fd-9f1436753740/OceanDNA-b16219.fa --refList OceanDNA-b16219/target_genomes.txt --output OceanDNA-b16219/fastani_result.tsv --threads 1
[2023-03-17 07:45:10,121] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:10,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:10,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:10,121] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:10,122] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:45:10,122] [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
--------------------------------------------------------------------------------
[2023-03-17 07:45:10,122] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16219/tc_result.tsv
[2023-03-17 07:45:10,122] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:10,122] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:10,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference/checkm_data
[2023-03-17 07:45:10,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:10,130] [INFO] Task started: CheckM
[2023-03-17 07:45:10,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16219/checkm_input OceanDNA-b16219/checkm_result
[2023-03-17 07:45:57,705] [INFO] Task succeeded: CheckM
[2023-03-17 07:45:57,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:45:57,708] [INFO] ===== Completeness check finished =====
[2023-03-17 07:45:57,708] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:45:57,708] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16219/markers.fasta)
[2023-03-17 07:45:57,709] [INFO] Task started: Blastn
[2023-03-17 07:45:57,709] [INFO] Running command: blastn -query OceanDNA-b16219/markers.fasta -db /var/lib/cwl/stg8932831e-2510-4d48-87c2-fbc173ab31c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:58,408] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:58,409] [INFO] Selected 22 target genomes.
[2023-03-17 07:45:58,409] [INFO] Target genome list was writen to OceanDNA-b16219/target_genomes_gtdb.txt
[2023-03-17 07:45:58,454] [INFO] Task started: fastANI
[2023-03-17 07:45:58,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b34f34d-0ad3-4e07-a7fd-9f1436753740/OceanDNA-b16219.fa --refList OceanDNA-b16219/target_genomes_gtdb.txt --output OceanDNA-b16219/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:11,816] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:11,821] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:46:11,821] [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_003242035.1	s__Phormidesmis foveolarum	76.7755	202	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314865.1	s__Phormidesmis priestleyi_B	76.6297	226	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242115.1	s__Phormidesmis priestleyi_A	76.4446	171	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207105.1	s__Phormidesmis sp015207105	76.4127	163	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155595.1	s__Phormidesmis sp000155595	76.3923	116	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033015.1	s__Phormidesmis sp012033015	76.3808	173	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286735.1	s__Phormidesmis sp002286735	76.3342	196	1101	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:11,821] [INFO] GTDB search result was written to OceanDNA-b16219/result_gtdb.tsv
[2023-03-17 07:46:11,821] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:11,822] [INFO] DFAST_QC result json was written to OceanDNA-b16219/dqc_result.json
[2023-03-17 07:46:11,822] [INFO] DFAST_QC completed!
[2023-03-17 07:46:11,822] [INFO] Total running time: 0h1m35s