[2023-03-18 20:13:32,185] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,185] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,185] [INFO] DQC Reference Directory: /var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference
[2023-03-18 20:13:33,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stgd40b3d9e-7038-46cc-9a28-1b6a0e09da4c/OceanDNA-b4027.fa | prodigal -d OceanDNA-b4027/cds.fna -a OceanDNA-b4027/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:50,423] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:50,424] [INFO] Task started: HMMsearch
[2023-03-18 20:13:50,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b4027/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference/reference_markers.hmm OceanDNA-b4027/protein.faa > /dev/null
[2023-03-18 20:13:50,635] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:50,636] [INFO] Found 6/6 markers.
[2023-03-18 20:13:50,662] [INFO] Query marker FASTA was written to OceanDNA-b4027/markers.fasta
[2023-03-18 20:13:50,662] [INFO] Task started: Blastn
[2023-03-18 20:13:50,662] [INFO] Running command: blastn -query OceanDNA-b4027/markers.fasta -db /var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference/reference_markers.fasta -out OceanDNA-b4027/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:51,243] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:51,244] [INFO] Selected 26 target genomes.
[2023-03-18 20:13:51,244] [INFO] Target genome list was writen to OceanDNA-b4027/target_genomes.txt
[2023-03-18 20:13:51,258] [INFO] Task started: fastANI
[2023-03-18 20:13:51,258] [INFO] Running command: fastANI --query /var/lib/cwl/stgd40b3d9e-7038-46cc-9a28-1b6a0e09da4c/OceanDNA-b4027.fa --refList OceanDNA-b4027/target_genomes.txt --output OceanDNA-b4027/fastani_result.tsv --threads 1
[2023-03-18 20:14:11,310] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:11,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:11,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:11,311] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:11,311] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:14:11,311] [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 20:14:11,311] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4027/tc_result.tsv
[2023-03-18 20:14:11,311] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:11,311] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:11,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference/checkm_data
[2023-03-18 20:14:11,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:11,319] [INFO] Task started: CheckM
[2023-03-18 20:14:11,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4027/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4027/checkm_input OceanDNA-b4027/checkm_result
[2023-03-18 20:14:58,098] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:58,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.62%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:58,101] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:58,101] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:58,101] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4027/markers.fasta)
[2023-03-18 20:14:58,101] [INFO] Task started: Blastn
[2023-03-18 20:14:58,101] [INFO] Running command: blastn -query OceanDNA-b4027/markers.fasta -db /var/lib/cwl/stg81fbe09c-ce69-416e-a104-86f22850a6b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4027/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:59,026] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:59,027] [INFO] Selected 21 target genomes.
[2023-03-18 20:14:59,027] [INFO] Target genome list was writen to OceanDNA-b4027/target_genomes_gtdb.txt
[2023-03-18 20:14:59,492] [INFO] Task started: fastANI
[2023-03-18 20:14:59,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgd40b3d9e-7038-46cc-9a28-1b6a0e09da4c/OceanDNA-b4027.fa --refList OceanDNA-b4027/target_genomes_gtdb.txt --output OceanDNA-b4027/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:13,840] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:13,846] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:15:13,846] [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_016787755.1	s__ELB16-189 sp016787755	82.5446	364	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787745.1	s__ELB16-189 sp016787745	79.2644	88	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712035.1	s__ELB16-189 sp016712035	77.2685	120	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709845.1	s__ELB16-189 sp016709845	77.2123	111	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013414665.1	s__ELB16-189 sp013414665	77.0806	70	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018063305.1	s__ELB16-189 sp018063305	77.0588	93	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303795.1	s__ELB16-189 sp017303795	76.8273	97	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787725.1	s__ELB16-189 sp016787725	76.7147	63	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001567185.1	s__ELB16-189 sp001567185	76.4243	74	486	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	98.67	98.67	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:13,846] [INFO] GTDB search result was written to OceanDNA-b4027/result_gtdb.tsv
[2023-03-18 20:15:13,847] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:13,847] [INFO] DFAST_QC result json was written to OceanDNA-b4027/dqc_result.json
[2023-03-18 20:15:13,848] [INFO] DFAST_QC completed!
[2023-03-18 20:15:13,848] [INFO] Total running time: 0h1m42s