[2023-03-18 08:55:50,572] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,572] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference
[2023-03-18 08:55:51,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,829] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,829] [INFO] Running command: cat /var/lib/cwl/stg82b84077-5fb9-4a6b-8f0e-82353813452b/OceanDNA-b16224.fa | prodigal -d OceanDNA-b16224/cds.fna -a OceanDNA-b16224/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:18,457] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:18,457] [INFO] Task started: HMMsearch
[2023-03-18 08:56:18,457] [INFO] Running command: hmmsearch --tblout OceanDNA-b16224/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference/reference_markers.hmm OceanDNA-b16224/protein.faa > /dev/null
[2023-03-18 08:56:18,758] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:18,759] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg82b84077-5fb9-4a6b-8f0e-82353813452b/OceanDNA-b16224.fa]
[2023-03-18 08:56:18,793] [INFO] Query marker FASTA was written to OceanDNA-b16224/markers.fasta
[2023-03-18 08:56:18,795] [INFO] Task started: Blastn
[2023-03-18 08:56:18,796] [INFO] Running command: blastn -query OceanDNA-b16224/markers.fasta -db /var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference/reference_markers.fasta -out OceanDNA-b16224/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:19,573] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:19,576] [INFO] Selected 26 target genomes.
[2023-03-18 08:56:19,576] [INFO] Target genome list was writen to OceanDNA-b16224/target_genomes.txt
[2023-03-18 08:56:19,597] [INFO] Task started: fastANI
[2023-03-18 08:56:19,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b84077-5fb9-4a6b-8f0e-82353813452b/OceanDNA-b16224.fa --refList OceanDNA-b16224/target_genomes.txt --output OceanDNA-b16224/fastani_result.tsv --threads 1
[2023-03-18 08:56:34,445] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:34,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:34,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:34,445] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:34,446] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:56:34,446] [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 08:56:34,446] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16224/tc_result.tsv
[2023-03-18 08:56:34,446] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:34,446] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:34,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference/checkm_data
[2023-03-18 08:56:34,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:34,456] [INFO] Task started: CheckM
[2023-03-18 08:56:34,456] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16224/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16224/checkm_input OceanDNA-b16224/checkm_result
[2023-03-18 08:57:39,582] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:39,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:39,587] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:39,587] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:39,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16224/markers.fasta)
[2023-03-18 08:57:39,589] [INFO] Task started: Blastn
[2023-03-18 08:57:39,589] [INFO] Running command: blastn -query OceanDNA-b16224/markers.fasta -db /var/lib/cwl/stgb638ea7d-8992-4259-87a1-f6bb9b8cf26a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16224/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:40,351] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:40,353] [INFO] Selected 20 target genomes.
[2023-03-18 08:57:40,353] [INFO] Target genome list was writen to OceanDNA-b16224/target_genomes_gtdb.txt
[2023-03-18 08:57:40,363] [INFO] Task started: fastANI
[2023-03-18 08:57:40,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b84077-5fb9-4a6b-8f0e-82353813452b/OceanDNA-b16224.fa --refList OceanDNA-b16224/target_genomes_gtdb.txt --output OceanDNA-b16224/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:56,564] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:56,572] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:57:56,572] [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	82.9425	941	1636	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	77.1983	258	1636	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	77.0213	279	1636	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	76.9842	329	1636	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	76.9779	311	1636	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	76.9041	250	1636	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	76.5256	178	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Phormidesmis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003017855.1	s__Nodosilinea sp003017855	75.6301	70	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCF_015207265.1	s__Nodosilinea sp015207265	75.5118	74	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207525.1	s__Nodosilinea sp015207525	75.4973	60	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016403105.1	s__Nodosilinea sp016403105	75.4305	50	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207395.1	s__Nodosilinea sp015207395	75.3857	74	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001548395.1	s__O-77 sp001548395	75.3073	61	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	95.35	95.35	0.93	0.93	2	-
GCA_003241845.1	s__Nodosilinea antarctica	75.1977	82	1636	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	98.34	98.34	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:56,573] [INFO] GTDB search result was written to OceanDNA-b16224/result_gtdb.tsv
[2023-03-18 08:57:56,573] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:56,574] [INFO] DFAST_QC result json was written to OceanDNA-b16224/dqc_result.json
[2023-03-18 08:57:56,574] [INFO] DFAST_QC completed!
[2023-03-18 08:57:56,574] [INFO] Total running time: 0h2m6s