[2023-03-18 23:18:18,430] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:18:18,430] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:18:18,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference
[2023-03-18 23:18:19,518] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:18:19,518] [INFO] Task started: Prodigal
[2023-03-18 23:18:19,518] [INFO] Running command: cat /var/lib/cwl/stgb117d9af-cfdf-4575-adf7-b6038bf57961/OceanDNA-b16046.fa | prodigal -d OceanDNA-b16046/cds.fna -a OceanDNA-b16046/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:18:51,156] [INFO] Task succeeded: Prodigal
[2023-03-18 23:18:51,157] [INFO] Task started: HMMsearch
[2023-03-18 23:18:51,157] [INFO] Running command: hmmsearch --tblout OceanDNA-b16046/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference/reference_markers.hmm OceanDNA-b16046/protein.faa > /dev/null
[2023-03-18 23:18:51,415] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:18:51,416] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb117d9af-cfdf-4575-adf7-b6038bf57961/OceanDNA-b16046.fa]
[2023-03-18 23:18:51,452] [INFO] Query marker FASTA was written to OceanDNA-b16046/markers.fasta
[2023-03-18 23:18:51,453] [INFO] Task started: Blastn
[2023-03-18 23:18:51,453] [INFO] Running command: blastn -query OceanDNA-b16046/markers.fasta -db /var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference/reference_markers.fasta -out OceanDNA-b16046/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:18:52,006] [INFO] Task succeeded: Blastn
[2023-03-18 23:18:52,007] [INFO] Selected 18 target genomes.
[2023-03-18 23:18:52,007] [INFO] Target genome list was writen to OceanDNA-b16046/target_genomes.txt
[2023-03-18 23:18:52,039] [INFO] Task started: fastANI
[2023-03-18 23:18:52,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgb117d9af-cfdf-4575-adf7-b6038bf57961/OceanDNA-b16046.fa --refList OceanDNA-b16046/target_genomes.txt --output OceanDNA-b16046/fastani_result.tsv --threads 1
[2023-03-18 23:19:06,822] [INFO] Task succeeded: fastANI
[2023-03-18 23:19:06,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:19:06,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:19:06,827] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:19:06,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:19:06,827] [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
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	76.0183	148	1776	95	below_threshold
Spirulina major	strain=PCC 6313	GCA_001890765.1	270636	270636	type	True	75.5172	62	1776	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.2141	82	1776	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:19:06,828] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16046/tc_result.tsv
[2023-03-18 23:19:06,828] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:19:06,828] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:19:06,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference/checkm_data
[2023-03-18 23:19:06,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:19:06,836] [INFO] Task started: CheckM
[2023-03-18 23:19:06,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16046/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16046/checkm_input OceanDNA-b16046/checkm_result
[2023-03-18 23:20:23,270] [INFO] Task succeeded: CheckM
[2023-03-18 23:20:23,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:20:23,274] [INFO] ===== Completeness check finished =====
[2023-03-18 23:20:23,274] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:20:23,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16046/markers.fasta)
[2023-03-18 23:20:23,276] [INFO] Task started: Blastn
[2023-03-18 23:20:23,276] [INFO] Running command: blastn -query OceanDNA-b16046/markers.fasta -db /var/lib/cwl/stg65824000-5f0e-4a54-8e87-595b556e66af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16046/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:20:24,144] [INFO] Task succeeded: Blastn
[2023-03-18 23:20:24,145] [INFO] Selected 17 target genomes.
[2023-03-18 23:20:24,145] [INFO] Target genome list was writen to OceanDNA-b16046/target_genomes_gtdb.txt
[2023-03-18 23:20:24,260] [INFO] Task started: fastANI
[2023-03-18 23:20:24,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgb117d9af-cfdf-4575-adf7-b6038bf57961/OceanDNA-b16046.fa --refList OceanDNA-b16046/target_genomes_gtdb.txt --output OceanDNA-b16046/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:20:39,209] [INFO] Task succeeded: fastANI
[2023-03-18 23:20:39,215] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:20:39,215] [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_015207075.1	s__LEGE-11467 sp015207075	81.7396	761	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__LEGE-11467	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015295945.1	s__DVED01 sp003695795	76.7917	273	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__DVED01	95.0	99.89	99.88	0.96	0.93	3	-
GCF_000332355.1	s__Geitlerinema sp000332355	76.0118	147	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Geitlerinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000380225.1	s__ESFC-1 sp000380225	75.9891	67	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__ESFC-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012295525.1	s__Oxynema aestuarii	75.9146	144	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oxynema	95.0	97.71	95.88	0.95	0.91	3	-
GCF_001637315.1	s__Phormidium_A willei_A	75.7615	77	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	95.56	95.56	0.82	0.82	2	-
GCA_010672965.1	s__SIO1A7 sp010672965	75.5852	104	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__SIO1A7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694125.1	s__RECH01 sp007694125	75.5659	50	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__RECH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890765.1	s__Spirulina major	75.5172	62	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276715.1	s__Planktothricoides sp001276715	75.3617	79	1776	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	99.30	99.29	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:20:39,216] [INFO] GTDB search result was written to OceanDNA-b16046/result_gtdb.tsv
[2023-03-18 23:20:39,216] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:20:39,217] [INFO] DFAST_QC result json was written to OceanDNA-b16046/dqc_result.json
[2023-03-18 23:20:39,217] [INFO] DFAST_QC completed!
[2023-03-18 23:20:39,217] [INFO] Total running time: 0h2m21s