[2023-03-14 13:16:07,190] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:16:07,190] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:16:07,190] [INFO] DQC Reference Directory: /var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference
[2023-03-14 13:16:08,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:16:08,280] [INFO] Task started: Prodigal
[2023-03-14 13:16:08,280] [INFO] Running command: cat /var/lib/cwl/stg17f09a2f-d0ff-4df2-b983-7166e4cd6c77/OceanDNA-b37748.fa | prodigal -d OceanDNA-b37748/cds.fna -a OceanDNA-b37748/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:16:16,819] [INFO] Task succeeded: Prodigal
[2023-03-14 13:16:16,819] [INFO] Task started: HMMsearch
[2023-03-14 13:16:16,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b37748/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference/reference_markers.hmm OceanDNA-b37748/protein.faa > /dev/null
[2023-03-14 13:16:16,979] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:16:16,979] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg17f09a2f-d0ff-4df2-b983-7166e4cd6c77/OceanDNA-b37748.fa]
[2023-03-14 13:16:16,993] [INFO] Query marker FASTA was written to OceanDNA-b37748/markers.fasta
[2023-03-14 13:16:16,994] [INFO] Task started: Blastn
[2023-03-14 13:16:16,994] [INFO] Running command: blastn -query OceanDNA-b37748/markers.fasta -db /var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference/reference_markers.fasta -out OceanDNA-b37748/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:16:17,602] [INFO] Task succeeded: Blastn
[2023-03-14 13:16:17,603] [INFO] Selected 29 target genomes.
[2023-03-14 13:16:17,603] [INFO] Target genome list was writen to OceanDNA-b37748/target_genomes.txt
[2023-03-14 13:16:17,645] [INFO] Task started: fastANI
[2023-03-14 13:16:17,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg17f09a2f-d0ff-4df2-b983-7166e4cd6c77/OceanDNA-b37748.fa --refList OceanDNA-b37748/target_genomes.txt --output OceanDNA-b37748/fastani_result.tsv --threads 1
[2023-03-14 13:16:35,284] [INFO] Task succeeded: fastANI
[2023-03-14 13:16:35,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:16:35,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:16:35,285] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:16:35,285] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:16:35,285] [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
--------------------------------------------------------------------------------
[2023-03-14 13:16:35,285] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37748/tc_result.tsv
[2023-03-14 13:16:35,285] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:16:35,285] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:16:35,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference/checkm_data
[2023-03-14 13:16:35,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:16:35,321] [INFO] Task started: CheckM
[2023-03-14 13:16:35,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37748/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37748/checkm_input OceanDNA-b37748/checkm_result
[2023-03-14 13:17:05,458] [INFO] Task succeeded: CheckM
[2023-03-14 13:17:05,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.62%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:17:05,461] [INFO] ===== Completeness check finished =====
[2023-03-14 13:17:05,461] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:17:05,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37748/markers.fasta)
[2023-03-14 13:17:05,462] [INFO] Task started: Blastn
[2023-03-14 13:17:05,462] [INFO] Running command: blastn -query OceanDNA-b37748/markers.fasta -db /var/lib/cwl/stga4601354-a288-4dcd-a9b7-71c00dd9f6ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37748/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:17:06,497] [INFO] Task succeeded: Blastn
[2023-03-14 13:17:06,498] [INFO] Selected 10 target genomes.
[2023-03-14 13:17:06,498] [INFO] Target genome list was writen to OceanDNA-b37748/target_genomes_gtdb.txt
[2023-03-14 13:17:06,513] [INFO] Task started: fastANI
[2023-03-14 13:17:06,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg17f09a2f-d0ff-4df2-b983-7166e4cd6c77/OceanDNA-b37748.fa --refList OceanDNA-b37748/target_genomes_gtdb.txt --output OceanDNA-b37748/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:17:12,882] [INFO] Task succeeded: fastANI
[2023-03-14 13:17:12,889] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:17:12,889] [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_902518075.1	s__Luminiphilus sp902518075	91.5746	197	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623175.1	s__Luminiphilus sp902623175	90.019	339	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520195.1	s__Luminiphilus sp902520195	88.3516	272	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_018222695.1	s__Luminiphilus sp018222695	85.587	271	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	85.4226	254	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331685.1	s__Luminiphilus sp003331685	84.748	194	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911345.1	s__Luminiphilus sp013911345	81.8173	114	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377985.1	s__Luminiphilus sp002377985	77.4622	105	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081075.1	s__Luminiphilus sp008081075	76.88	63	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:17:12,889] [INFO] GTDB search result was written to OceanDNA-b37748/result_gtdb.tsv
[2023-03-14 13:17:12,889] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:17:12,890] [INFO] DFAST_QC result json was written to OceanDNA-b37748/dqc_result.json
[2023-03-14 13:17:12,890] [INFO] DFAST_QC completed!
[2023-03-14 13:17:12,890] [INFO] Total running time: 0h1m6s