[2023-03-17 05:39:41,241] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:39:41,241] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:39:41,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference
[2023-03-17 05:39:42,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:39:42,366] [INFO] Task started: Prodigal
[2023-03-17 05:39:42,366] [INFO] Running command: cat /var/lib/cwl/stgedbfe491-a617-484f-b244-d9527dd8e9b5/OceanDNA-b36670.fa | prodigal -d OceanDNA-b36670/cds.fna -a OceanDNA-b36670/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:40:08,768] [INFO] Task succeeded: Prodigal
[2023-03-17 05:40:08,769] [INFO] Task started: HMMsearch
[2023-03-17 05:40:08,769] [INFO] Running command: hmmsearch --tblout OceanDNA-b36670/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference/reference_markers.hmm OceanDNA-b36670/protein.faa > /dev/null
[2023-03-17 05:40:09,000] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:40:09,001] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgedbfe491-a617-484f-b244-d9527dd8e9b5/OceanDNA-b36670.fa]
[2023-03-17 05:40:09,027] [INFO] Query marker FASTA was written to OceanDNA-b36670/markers.fasta
[2023-03-17 05:40:09,028] [INFO] Task started: Blastn
[2023-03-17 05:40:09,028] [INFO] Running command: blastn -query OceanDNA-b36670/markers.fasta -db /var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference/reference_markers.fasta -out OceanDNA-b36670/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:40:09,563] [INFO] Task succeeded: Blastn
[2023-03-17 05:40:09,564] [INFO] Selected 13 target genomes.
[2023-03-17 05:40:09,564] [INFO] Target genome list was writen to OceanDNA-b36670/target_genomes.txt
[2023-03-17 05:40:09,573] [INFO] Task started: fastANI
[2023-03-17 05:40:09,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgedbfe491-a617-484f-b244-d9527dd8e9b5/OceanDNA-b36670.fa --refList OceanDNA-b36670/target_genomes.txt --output OceanDNA-b36670/fastani_result.tsv --threads 1
[2023-03-17 05:40:18,415] [INFO] Task succeeded: fastANI
[2023-03-17 05:40:18,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:40:18,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:40:18,421] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:40:18,421] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:40:18,421] [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
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	78.1149	194	1483	95	below_threshold
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	77.4296	197	1483	95	below_threshold
Pseudoteredinibacter isoporae	strain=LMG 25246	GCA_011602085.1	570281	570281	type	True	76.9245	81	1483	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_014207695.1	570281	570281	type	True	76.8968	82	1483	95	below_threshold
Pseudoteredinibacter isoporae	strain=DSM 22368	GCA_011683895.1	570281	570281	type	True	76.8952	80	1483	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.7278	59	1483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:40:18,421] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36670/tc_result.tsv
[2023-03-17 05:40:18,421] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:40:18,421] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:40:18,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference/checkm_data
[2023-03-17 05:40:18,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:40:18,428] [INFO] Task started: CheckM
[2023-03-17 05:40:18,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36670/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36670/checkm_input OceanDNA-b36670/checkm_result
[2023-03-17 05:41:23,892] [INFO] Task succeeded: CheckM
[2023-03-17 05:41:23,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:41:23,895] [INFO] ===== Completeness check finished =====
[2023-03-17 05:41:23,896] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:41:23,896] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36670/markers.fasta)
[2023-03-17 05:41:23,897] [INFO] Task started: Blastn
[2023-03-17 05:41:23,897] [INFO] Running command: blastn -query OceanDNA-b36670/markers.fasta -db /var/lib/cwl/stg4096069e-5abb-4566-8aa1-2ca7200d098e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36670/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:41:24,591] [INFO] Task succeeded: Blastn
[2023-03-17 05:41:24,591] [INFO] Selected 14 target genomes.
[2023-03-17 05:41:24,591] [INFO] Target genome list was writen to OceanDNA-b36670/target_genomes_gtdb.txt
[2023-03-17 05:41:24,623] [INFO] Task started: fastANI
[2023-03-17 05:41:24,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgedbfe491-a617-484f-b244-d9527dd8e9b5/OceanDNA-b36670.fa --refList OceanDNA-b36670/target_genomes_gtdb.txt --output OceanDNA-b36670/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:41:35,308] [INFO] Task succeeded: fastANI
[2023-03-17 05:41:35,313] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:41:35,313] [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_002707785.1	s__Pseudomaricurvus sp002707785	99.7715	1396	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	99.83	99.83	0.94	0.94	2	conclusive
GCF_018863235.1	s__Pseudomaricurvus sp018863235	78.1149	194	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	77.9	182	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	77.4316	196	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011602085.1	s__Pseudoteredinibacter isoporae	76.9245	81	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudoteredinibacter	95.0	100.00	100.00	1.00	0.99	3	-
GCF_000377745.1	s__Gilvimarinus chinensis	76.7659	58	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Gilvimarinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:41:35,313] [INFO] GTDB search result was written to OceanDNA-b36670/result_gtdb.tsv
[2023-03-17 05:41:35,313] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:41:35,314] [INFO] DFAST_QC result json was written to OceanDNA-b36670/dqc_result.json
[2023-03-17 05:41:35,314] [INFO] DFAST_QC completed!
[2023-03-17 05:41:35,314] [INFO] Total running time: 0h1m54s