[2023-03-14 14:59:36,895] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:59:36,895] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:59:36,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference
[2023-03-14 14:59:38,199] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:59:38,200] [INFO] Task started: Prodigal
[2023-03-14 14:59:38,201] [INFO] Running command: cat /var/lib/cwl/stg8916a8a2-56ab-4e22-86ff-d9501b9e74fc/OceanDNA-b42035.fa | prodigal -d OceanDNA-b42035/cds.fna -a OceanDNA-b42035/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:59:46,513] [INFO] Task succeeded: Prodigal
[2023-03-14 14:59:46,513] [INFO] Task started: HMMsearch
[2023-03-14 14:59:46,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b42035/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference/reference_markers.hmm OceanDNA-b42035/protein.faa > /dev/null
[2023-03-14 14:59:46,882] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:59:46,883] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8916a8a2-56ab-4e22-86ff-d9501b9e74fc/OceanDNA-b42035.fa]
[2023-03-14 14:59:46,893] [INFO] Query marker FASTA was written to OceanDNA-b42035/markers.fasta
[2023-03-14 14:59:46,896] [INFO] Task started: Blastn
[2023-03-14 14:59:46,896] [INFO] Running command: blastn -query OceanDNA-b42035/markers.fasta -db /var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference/reference_markers.fasta -out OceanDNA-b42035/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:59:48,413] [INFO] Task succeeded: Blastn
[2023-03-14 14:59:48,414] [INFO] Selected 6 target genomes.
[2023-03-14 14:59:48,415] [INFO] Target genome list was writen to OceanDNA-b42035/target_genomes.txt
[2023-03-14 14:59:48,423] [INFO] Task started: fastANI
[2023-03-14 14:59:48,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg8916a8a2-56ab-4e22-86ff-d9501b9e74fc/OceanDNA-b42035.fa --refList OceanDNA-b42035/target_genomes.txt --output OceanDNA-b42035/fastani_result.tsv --threads 1
[2023-03-14 14:59:53,537] [INFO] Task succeeded: fastANI
[2023-03-14 14:59:53,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:59:53,538] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:59:53,538] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:59:53,538] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:59:53,538] [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 14:59:53,539] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42035/tc_result.tsv
[2023-03-14 14:59:53,539] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:59:53,539] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:59:53,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference/checkm_data
[2023-03-14 14:59:53,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:59:53,682] [INFO] Task started: CheckM
[2023-03-14 14:59:53,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42035/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42035/checkm_input OceanDNA-b42035/checkm_result
[2023-03-14 15:00:15,995] [INFO] Task succeeded: CheckM
[2023-03-14 15:00:15,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 15:00:15,998] [INFO] ===== Completeness check finished =====
[2023-03-14 15:00:15,998] [INFO] ===== Start GTDB Search =====
[2023-03-14 15:00:15,998] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42035/markers.fasta)
[2023-03-14 15:00:15,999] [INFO] Task started: Blastn
[2023-03-14 15:00:16,000] [INFO] Running command: blastn -query OceanDNA-b42035/markers.fasta -db /var/lib/cwl/stgd11b06d8-a499-472a-a985-4c02eba71642/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42035/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:00:16,911] [INFO] Task succeeded: Blastn
[2023-03-14 15:00:16,913] [INFO] Selected 22 target genomes.
[2023-03-14 15:00:16,913] [INFO] Target genome list was writen to OceanDNA-b42035/target_genomes_gtdb.txt
[2023-03-14 15:00:16,935] [INFO] Task started: fastANI
[2023-03-14 15:00:16,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg8916a8a2-56ab-4e22-86ff-d9501b9e74fc/OceanDNA-b42035.fa --refList OceanDNA-b42035/target_genomes_gtdb.txt --output OceanDNA-b42035/fastani_result_gtdb.tsv --threads 1
[2023-03-14 15:00:22,752] [INFO] Task succeeded: fastANI
[2023-03-14 15:00:22,758] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 15:00:22,758] [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_905478015.1	s__CAJQGY01 sp905478015	82.455	210	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__CAJQGY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	76.9139	70	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	76.7284	66	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478035.1	s__SCGC-AAA076-P13 sp905478035	76.6661	71	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515155.1	s__SCGC-AAA076-P13 sp902515155	76.6596	51	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	76.4746	61	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	76.4699	59	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	76.4409	71	305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-14 15:00:22,758] [INFO] GTDB search result was written to OceanDNA-b42035/result_gtdb.tsv
[2023-03-14 15:00:22,758] [INFO] ===== GTDB Search completed =====
[2023-03-14 15:00:22,760] [INFO] DFAST_QC result json was written to OceanDNA-b42035/dqc_result.json
[2023-03-14 15:00:22,760] [INFO] DFAST_QC completed!
[2023-03-14 15:00:22,760] [INFO] Total running time: 0h0m46s