[2023-03-18 10:15:15,040] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:15:15,040] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:15:15,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference
[2023-03-18 10:15:16,172] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:15:16,172] [INFO] Task started: Prodigal
[2023-03-18 10:15:16,172] [INFO] Running command: cat /var/lib/cwl/stg8e026ad5-2c43-4509-a598-5b95adfd219e/OceanDNA-b36273.fa | prodigal -d OceanDNA-b36273/cds.fna -a OceanDNA-b36273/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:15:24,466] [INFO] Task succeeded: Prodigal
[2023-03-18 10:15:24,466] [INFO] Task started: HMMsearch
[2023-03-18 10:15:24,466] [INFO] Running command: hmmsearch --tblout OceanDNA-b36273/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference/reference_markers.hmm OceanDNA-b36273/protein.faa > /dev/null
[2023-03-18 10:15:24,671] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:15:24,672] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8e026ad5-2c43-4509-a598-5b95adfd219e/OceanDNA-b36273.fa]
[2023-03-18 10:15:24,685] [INFO] Query marker FASTA was written to OceanDNA-b36273/markers.fasta
[2023-03-18 10:15:24,686] [INFO] Task started: Blastn
[2023-03-18 10:15:24,686] [INFO] Running command: blastn -query OceanDNA-b36273/markers.fasta -db /var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference/reference_markers.fasta -out OceanDNA-b36273/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:15:25,213] [INFO] Task succeeded: Blastn
[2023-03-18 10:15:25,213] [INFO] Selected 27 target genomes.
[2023-03-18 10:15:25,214] [INFO] Target genome list was writen to OceanDNA-b36273/target_genomes.txt
[2023-03-18 10:15:25,234] [INFO] Task started: fastANI
[2023-03-18 10:15:25,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e026ad5-2c43-4509-a598-5b95adfd219e/OceanDNA-b36273.fa --refList OceanDNA-b36273/target_genomes.txt --output OceanDNA-b36273/fastani_result.tsv --threads 1
[2023-03-18 10:15:40,161] [INFO] Task succeeded: fastANI
[2023-03-18 10:15:40,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:15:40,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:15:40,165] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:15:40,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:15:40,165] [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
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	76.8363	53	489	95	below_threshold
Methylophaga sulfidovorans	strain=DSM 11578	GCA_900114205.1	45496	45496	type	True	76.357	61	489	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:15:40,165] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36273/tc_result.tsv
[2023-03-18 10:15:40,165] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:15:40,165] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:15:40,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference/checkm_data
[2023-03-18 10:15:40,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:15:40,169] [INFO] Task started: CheckM
[2023-03-18 10:15:40,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36273/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36273/checkm_input OceanDNA-b36273/checkm_result
[2023-03-18 10:16:06,460] [INFO] Task succeeded: CheckM
[2023-03-18 10:16:06,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 2.78%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:16:06,470] [INFO] ===== Completeness check finished =====
[2023-03-18 10:16:06,470] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:16:06,470] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36273/markers.fasta)
[2023-03-18 10:16:06,471] [INFO] Task started: Blastn
[2023-03-18 10:16:06,471] [INFO] Running command: blastn -query OceanDNA-b36273/markers.fasta -db /var/lib/cwl/stg0b073f2c-9129-4d52-9fe6-129ac6b7098e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36273/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:16:07,229] [INFO] Task succeeded: Blastn
[2023-03-18 10:16:07,234] [INFO] Selected 15 target genomes.
[2023-03-18 10:16:07,235] [INFO] Target genome list was writen to OceanDNA-b36273/target_genomes_gtdb.txt
[2023-03-18 10:16:07,250] [INFO] Task started: fastANI
[2023-03-18 10:16:07,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e026ad5-2c43-4509-a598-5b95adfd219e/OceanDNA-b36273.fa --refList OceanDNA-b36273/target_genomes_gtdb.txt --output OceanDNA-b36273/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:16:13,578] [INFO] Task succeeded: fastANI
[2023-03-18 10:16:13,585] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:16:13,585] [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_018646825.1	s__GCA-002733105 sp018646825	99.6696	419	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479985.1	s__GCA-002733105 sp905479985	82.1115	377	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479075.1	s__GCA-002733105 sp905479075	78.1527	125	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181885.1	s__GCA-002733105 sp905181885	77.9042	112	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215775.1	s__GCA-002733105 sp013215775	77.5991	79	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733335.1	s__GCA-002733105 sp002733335	77.3878	57	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215825.1	s__GCA-002733105 sp013215825	76.9484	92	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214595.1	s__Methylophaga aminisulfidivorans	76.8336	54	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	97.12	97.07	0.93	0.92	4	-
GCA_002733715.2	s__GCA-002733105 sp002733715	76.6426	84	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163115.1	s__41-12-T18 sp002163115	76.5503	88	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733505.1	s__GCA-002733105 sp002733505	76.4724	77	489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:16:13,588] [INFO] GTDB search result was written to OceanDNA-b36273/result_gtdb.tsv
[2023-03-18 10:16:13,589] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:16:13,592] [INFO] DFAST_QC result json was written to OceanDNA-b36273/dqc_result.json
[2023-03-18 10:16:13,592] [INFO] DFAST_QC completed!
[2023-03-18 10:16:13,592] [INFO] Total running time: 0h0m59s