[2023-03-17 23:15:40,537] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:15:40,537] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:15:40,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference
[2023-03-17 23:15:41,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:15:41,641] [INFO] Task started: Prodigal
[2023-03-17 23:15:41,641] [INFO] Running command: cat /var/lib/cwl/stg6584a503-b3c4-4466-b4fa-07b2fceab367/OceanDNA-b4156.fa | prodigal -d OceanDNA-b4156/cds.fna -a OceanDNA-b4156/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:15:58,049] [INFO] Task succeeded: Prodigal
[2023-03-17 23:15:58,050] [INFO] Task started: HMMsearch
[2023-03-17 23:15:58,050] [INFO] Running command: hmmsearch --tblout OceanDNA-b4156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference/reference_markers.hmm OceanDNA-b4156/protein.faa > /dev/null
[2023-03-17 23:15:58,234] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:15:58,235] [INFO] Found 6/6 markers.
[2023-03-17 23:15:58,257] [INFO] Query marker FASTA was written to OceanDNA-b4156/markers.fasta
[2023-03-17 23:15:58,258] [INFO] Task started: Blastn
[2023-03-17 23:15:58,258] [INFO] Running command: blastn -query OceanDNA-b4156/markers.fasta -db /var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference/reference_markers.fasta -out OceanDNA-b4156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:15:58,784] [INFO] Task succeeded: Blastn
[2023-03-17 23:15:58,786] [INFO] Selected 22 target genomes.
[2023-03-17 23:15:58,786] [INFO] Target genome list was writen to OceanDNA-b4156/target_genomes.txt
[2023-03-17 23:15:58,793] [INFO] Task started: fastANI
[2023-03-17 23:15:58,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg6584a503-b3c4-4466-b4fa-07b2fceab367/OceanDNA-b4156.fa --refList OceanDNA-b4156/target_genomes.txt --output OceanDNA-b4156/fastani_result.tsv --threads 1
[2023-03-17 23:16:18,266] [INFO] Task succeeded: fastANI
[2023-03-17 23:16:18,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:16:18,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:16:18,270] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:16:18,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:16:18,271] [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
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	77.0476	69	645	95	below_threshold
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	76.7648	54	645	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:16:18,272] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4156/tc_result.tsv
[2023-03-17 23:16:18,273] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:16:18,273] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:16:18,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference/checkm_data
[2023-03-17 23:16:18,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:16:18,280] [INFO] Task started: CheckM
[2023-03-17 23:16:18,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4156/checkm_input OceanDNA-b4156/checkm_result
[2023-03-17 23:17:04,299] [INFO] Task succeeded: CheckM
[2023-03-17 23:17:04,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:17:04,304] [INFO] ===== Completeness check finished =====
[2023-03-17 23:17:04,304] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:17:04,304] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4156/markers.fasta)
[2023-03-17 23:17:04,305] [INFO] Task started: Blastn
[2023-03-17 23:17:04,305] [INFO] Running command: blastn -query OceanDNA-b4156/markers.fasta -db /var/lib/cwl/stgdfbac746-aff7-463f-bd07-b8d238c5fcff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:17:05,123] [INFO] Task succeeded: Blastn
[2023-03-17 23:17:05,124] [INFO] Selected 27 target genomes.
[2023-03-17 23:17:05,124] [INFO] Target genome list was writen to OceanDNA-b4156/target_genomes_gtdb.txt
[2023-03-17 23:17:05,140] [INFO] Task started: fastANI
[2023-03-17 23:17:05,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg6584a503-b3c4-4466-b4fa-07b2fceab367/OceanDNA-b4156.fa --refList OceanDNA-b4156/target_genomes_gtdb.txt --output OceanDNA-b4156/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:17:27,094] [INFO] Task succeeded: fastANI
[2023-03-17 23:17:27,096] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:17:27,096] [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_017068455.1	s__Fulvivirga sp017068455	77.0476	69	645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711525.1	s__Fulvivirga lutimaris	76.7648	54	645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:17:27,097] [INFO] GTDB search result was written to OceanDNA-b4156/result_gtdb.tsv
[2023-03-17 23:17:27,097] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:17:27,097] [INFO] DFAST_QC result json was written to OceanDNA-b4156/dqc_result.json
[2023-03-17 23:17:27,097] [INFO] DFAST_QC completed!
[2023-03-17 23:17:27,097] [INFO] Total running time: 0h1m47s