[2023-03-14 12:25:41,432] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference
[2023-03-14 12:25:42,604] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,604] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,605] [INFO] Running command: cat /var/lib/cwl/stg44200049-7f2f-420b-a19f-74b997f2362d/OceanDNA-b16218.fa | prodigal -d OceanDNA-b16218/cds.fna -a OceanDNA-b16218/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:26:00,165] [INFO] Task succeeded: Prodigal
[2023-03-14 12:26:00,165] [INFO] Task started: HMMsearch
[2023-03-14 12:26:00,165] [INFO] Running command: hmmsearch --tblout OceanDNA-b16218/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference/reference_markers.hmm OceanDNA-b16218/protein.faa > /dev/null
[2023-03-14 12:26:00,415] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:26:00,416] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg44200049-7f2f-420b-a19f-74b997f2362d/OceanDNA-b16218.fa]
[2023-03-14 12:26:00,446] [INFO] Query marker FASTA was written to OceanDNA-b16218/markers.fasta
[2023-03-14 12:26:00,446] [INFO] Task started: Blastn
[2023-03-14 12:26:00,446] [INFO] Running command: blastn -query OceanDNA-b16218/markers.fasta -db /var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference/reference_markers.fasta -out OceanDNA-b16218/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:00,999] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:01,000] [INFO] Selected 16 target genomes.
[2023-03-14 12:26:01,000] [INFO] Target genome list was writen to OceanDNA-b16218/target_genomes.txt
[2023-03-14 12:26:01,012] [INFO] Task started: fastANI
[2023-03-14 12:26:01,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg44200049-7f2f-420b-a19f-74b997f2362d/OceanDNA-b16218.fa --refList OceanDNA-b16218/target_genomes.txt --output OceanDNA-b16218/fastani_result.tsv --threads 1
[2023-03-14 12:26:13,588] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:13,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:13,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:13,588] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:13,588] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:26:13,588] [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 12:26:13,627] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16218/tc_result.tsv
[2023-03-14 12:26:13,627] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:13,627] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:13,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference/checkm_data
[2023-03-14 12:26:13,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:13,649] [INFO] Task started: CheckM
[2023-03-14 12:26:13,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16218/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16218/checkm_input OceanDNA-b16218/checkm_result
[2023-03-14 12:27:00,426] [INFO] Task succeeded: CheckM
[2023-03-14 12:27:00,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 12:27:00,429] [INFO] ===== Completeness check finished =====
[2023-03-14 12:27:00,429] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:27:00,429] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16218/markers.fasta)
[2023-03-14 12:27:00,429] [INFO] Task started: Blastn
[2023-03-14 12:27:00,429] [INFO] Running command: blastn -query OceanDNA-b16218/markers.fasta -db /var/lib/cwl/stg811ca354-ec6b-41b2-a9c8-739e8274fd58/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16218/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:01,192] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:01,192] [INFO] Selected 23 target genomes.
[2023-03-14 12:27:01,192] [INFO] Target genome list was writen to OceanDNA-b16218/target_genomes_gtdb.txt
[2023-03-14 12:27:01,212] [INFO] Task started: fastANI
[2023-03-14 12:27:01,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg44200049-7f2f-420b-a19f-74b997f2362d/OceanDNA-b16218.fa --refList OceanDNA-b16218/target_genomes_gtdb.txt --output OceanDNA-b16218/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:17,147] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:17,152] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:27:17,152] [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	76.7184	180	1060	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	76.6384	177	1060	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	76.629	147	1060	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	76.5826	185	1060	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	76.452	209	1060	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	76.3411	158	1060	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	76.1262	113	1060	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:17,152] [INFO] GTDB search result was written to OceanDNA-b16218/result_gtdb.tsv
[2023-03-14 12:27:17,152] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:17,153] [INFO] DFAST_QC result json was written to OceanDNA-b16218/dqc_result.json
[2023-03-14 12:27:17,153] [INFO] DFAST_QC completed!
[2023-03-14 12:27:17,153] [INFO] Total running time: 0h1m36s