[2023-03-15 03:14:16,421] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference
[2023-03-15 03:14:17,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,725] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,725] [INFO] Running command: cat /var/lib/cwl/stge02cb846-19fb-4ce3-a761-a851eaaf8841/OceanDNA-b30043.fa | prodigal -d OceanDNA-b30043/cds.fna -a OceanDNA-b30043/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:30,661] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:30,662] [INFO] Task started: HMMsearch
[2023-03-15 03:14:30,662] [INFO] Running command: hmmsearch --tblout OceanDNA-b30043/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference/reference_markers.hmm OceanDNA-b30043/protein.faa > /dev/null
[2023-03-15 03:14:30,872] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:30,873] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge02cb846-19fb-4ce3-a761-a851eaaf8841/OceanDNA-b30043.fa]
[2023-03-15 03:14:30,895] [INFO] Query marker FASTA was written to OceanDNA-b30043/markers.fasta
[2023-03-15 03:14:30,895] [INFO] Task started: Blastn
[2023-03-15 03:14:30,895] [INFO] Running command: blastn -query OceanDNA-b30043/markers.fasta -db /var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference/reference_markers.fasta -out OceanDNA-b30043/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:31,510] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:31,511] [INFO] Selected 30 target genomes.
[2023-03-15 03:14:31,512] [INFO] Target genome list was writen to OceanDNA-b30043/target_genomes.txt
[2023-03-15 03:14:31,527] [INFO] Task started: fastANI
[2023-03-15 03:14:31,528] [INFO] Running command: fastANI --query /var/lib/cwl/stge02cb846-19fb-4ce3-a761-a851eaaf8841/OceanDNA-b30043.fa --refList OceanDNA-b30043/target_genomes.txt --output OceanDNA-b30043/fastani_result.tsv --threads 1
[2023-03-15 03:14:48,687] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:48,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:48,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:48,691] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:48,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:14:48,691] [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
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	75.9783	58	571	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	75.7499	52	571	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:14:48,692] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30043/tc_result.tsv
[2023-03-15 03:14:48,692] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:48,692] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:48,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference/checkm_data
[2023-03-15 03:14:48,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:48,703] [INFO] Task started: CheckM
[2023-03-15 03:14:48,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30043/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30043/checkm_input OceanDNA-b30043/checkm_result
[2023-03-15 03:15:24,738] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:24,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:24,741] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:24,741] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:24,742] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30043/markers.fasta)
[2023-03-15 03:15:24,742] [INFO] Task started: Blastn
[2023-03-15 03:15:24,742] [INFO] Running command: blastn -query OceanDNA-b30043/markers.fasta -db /var/lib/cwl/stgf4e76871-2cbf-4e11-8088-48625529420f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30043/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:25,897] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:25,898] [INFO] Selected 28 target genomes.
[2023-03-15 03:15:25,898] [INFO] Target genome list was writen to OceanDNA-b30043/target_genomes_gtdb.txt
[2023-03-15 03:15:25,922] [INFO] Task started: fastANI
[2023-03-15 03:15:25,922] [INFO] Running command: fastANI --query /var/lib/cwl/stge02cb846-19fb-4ce3-a761-a851eaaf8841/OceanDNA-b30043.fa --refList OceanDNA-b30043/target_genomes_gtdb.txt --output OceanDNA-b30043/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:43,151] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:43,157] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:43,157] [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
GCF_001078595.1	s__Rhodobacter_B lobularis	76.6343	98	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184935.1	s__Actibacterium_A lipolyticum	75.9783	58	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	75.8056	55	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	75.7977	59	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_002285435.1	s__Actibacterium ureilyticum	75.7832	58	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	75.7499	52	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	75.6817	58	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065155.1	s__SW4 sp002732825	75.6738	61	571	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:43,157] [INFO] GTDB search result was written to OceanDNA-b30043/result_gtdb.tsv
[2023-03-15 03:15:43,157] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:43,158] [INFO] DFAST_QC result json was written to OceanDNA-b30043/dqc_result.json
[2023-03-15 03:15:43,158] [INFO] DFAST_QC completed!
[2023-03-15 03:15:43,158] [INFO] Total running time: 0h1m27s