[2023-03-18 01:24:53,314] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:24:53,314] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:24:53,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference
[2023-03-18 01:24:54,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:24:54,432] [INFO] Task started: Prodigal
[2023-03-18 01:24:54,432] [INFO] Running command: cat /var/lib/cwl/stg7e893e79-74c5-4e3c-911c-f348fd19e676/OceanDNA-b43873.fa | prodigal -d OceanDNA-b43873/cds.fna -a OceanDNA-b43873/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:25:15,174] [INFO] Task succeeded: Prodigal
[2023-03-18 01:25:15,175] [INFO] Task started: HMMsearch
[2023-03-18 01:25:15,175] [INFO] Running command: hmmsearch --tblout OceanDNA-b43873/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference/reference_markers.hmm OceanDNA-b43873/protein.faa > /dev/null
[2023-03-18 01:25:15,391] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:25:15,391] [INFO] Found 6/6 markers.
[2023-03-18 01:25:15,411] [INFO] Query marker FASTA was written to OceanDNA-b43873/markers.fasta
[2023-03-18 01:25:15,412] [INFO] Task started: Blastn
[2023-03-18 01:25:15,412] [INFO] Running command: blastn -query OceanDNA-b43873/markers.fasta -db /var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference/reference_markers.fasta -out OceanDNA-b43873/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:25:16,008] [INFO] Task succeeded: Blastn
[2023-03-18 01:25:16,009] [INFO] Selected 27 target genomes.
[2023-03-18 01:25:16,009] [INFO] Target genome list was writen to OceanDNA-b43873/target_genomes.txt
[2023-03-18 01:25:16,049] [INFO] Task started: fastANI
[2023-03-18 01:25:16,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e893e79-74c5-4e3c-911c-f348fd19e676/OceanDNA-b43873.fa --refList OceanDNA-b43873/target_genomes.txt --output OceanDNA-b43873/fastani_result.tsv --threads 1
[2023-03-18 01:25:34,121] [INFO] Task succeeded: fastANI
[2023-03-18 01:25:34,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:25:34,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:25:34,125] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:25:34,125] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:25:34,125] [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
Arenicella chitinivorans	strain=KCTC 12711	GCA_014651515.1	1329800	1329800	type	True	82.5346	790	1082	95	below_threshold
Arenicella xantha	strain=DSM 24032	GCA_003315245.1	644221	644221	type	True	77.4077	143	1082	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:25:34,125] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43873/tc_result.tsv
[2023-03-18 01:25:34,125] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:25:34,125] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:25:34,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference/checkm_data
[2023-03-18 01:25:34,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:25:34,131] [INFO] Task started: CheckM
[2023-03-18 01:25:34,131] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43873/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43873/checkm_input OceanDNA-b43873/checkm_result
[2023-03-18 01:26:28,235] [INFO] Task succeeded: CheckM
[2023-03-18 01:26:28,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:26:28,238] [INFO] ===== Completeness check finished =====
[2023-03-18 01:26:28,238] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:26:28,239] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43873/markers.fasta)
[2023-03-18 01:26:28,240] [INFO] Task started: Blastn
[2023-03-18 01:26:28,240] [INFO] Running command: blastn -query OceanDNA-b43873/markers.fasta -db /var/lib/cwl/stg75d94c69-d2f0-489a-863a-63535076030d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43873/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:29,217] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:29,218] [INFO] Selected 25 target genomes.
[2023-03-18 01:26:29,218] [INFO] Target genome list was writen to OceanDNA-b43873/target_genomes_gtdb.txt
[2023-03-18 01:26:29,402] [INFO] Task started: fastANI
[2023-03-18 01:26:29,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e893e79-74c5-4e3c-911c-f348fd19e676/OceanDNA-b43873.fa --refList OceanDNA-b43873/target_genomes_gtdb.txt --output OceanDNA-b43873/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:26:44,667] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:44,671] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:26:44,671] [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_014651515.1	s__Arenicella chitinivorans	82.5342	790	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315245.1	s__Arenicella xantha	77.4077	143	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854775.1	s__Arenicella sp017854775	76.7447	52	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002025.1	s__Arenicella sp013002025	76.6676	59	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:26:44,671] [INFO] GTDB search result was written to OceanDNA-b43873/result_gtdb.tsv
[2023-03-18 01:26:44,672] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:26:44,672] [INFO] DFAST_QC result json was written to OceanDNA-b43873/dqc_result.json
[2023-03-18 01:26:44,672] [INFO] DFAST_QC completed!
[2023-03-18 01:26:44,672] [INFO] Total running time: 0h1m51s