[2023-03-15 03:38:34,774] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:38:34,775] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:38:34,775] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference
[2023-03-15 03:38:35,915] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:38:35,915] [INFO] Task started: Prodigal
[2023-03-15 03:38:35,915] [INFO] Running command: cat /var/lib/cwl/stg52745dec-0f4b-4da4-85d7-e7bb9046c5db/OceanDNA-b37852.fa | prodigal -d OceanDNA-b37852/cds.fna -a OceanDNA-b37852/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:38:44,751] [INFO] Task succeeded: Prodigal
[2023-03-15 03:38:44,752] [INFO] Task started: HMMsearch
[2023-03-15 03:38:44,752] [INFO] Running command: hmmsearch --tblout OceanDNA-b37852/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference/reference_markers.hmm OceanDNA-b37852/protein.faa > /dev/null
[2023-03-15 03:38:44,909] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:38:44,910] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg52745dec-0f4b-4da4-85d7-e7bb9046c5db/OceanDNA-b37852.fa]
[2023-03-15 03:38:44,930] [INFO] Query marker FASTA was written to OceanDNA-b37852/markers.fasta
[2023-03-15 03:38:44,944] [INFO] Task started: Blastn
[2023-03-15 03:38:44,944] [INFO] Running command: blastn -query OceanDNA-b37852/markers.fasta -db /var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference/reference_markers.fasta -out OceanDNA-b37852/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:38:45,545] [INFO] Task succeeded: Blastn
[2023-03-15 03:38:45,548] [INFO] Selected 15 target genomes.
[2023-03-15 03:38:45,548] [INFO] Target genome list was writen to OceanDNA-b37852/target_genomes.txt
[2023-03-15 03:38:45,576] [INFO] Task started: fastANI
[2023-03-15 03:38:45,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg52745dec-0f4b-4da4-85d7-e7bb9046c5db/OceanDNA-b37852.fa --refList OceanDNA-b37852/target_genomes.txt --output OceanDNA-b37852/fastani_result.tsv --threads 1
[2023-03-15 03:38:56,129] [INFO] Task succeeded: fastANI
[2023-03-15 03:38:56,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:38:56,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:38:56,130] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:38:56,130] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:38:56,130] [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
--------------------------------------------------------------------------------
[2023-03-15 03:38:56,131] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37852/tc_result.tsv
[2023-03-15 03:38:56,131] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:38:56,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:38:56,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference/checkm_data
[2023-03-15 03:38:56,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:38:56,240] [INFO] Task started: CheckM
[2023-03-15 03:38:56,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37852/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37852/checkm_input OceanDNA-b37852/checkm_result
[2023-03-15 03:39:26,130] [INFO] Task succeeded: CheckM
[2023-03-15 03:39:26,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:39:26,134] [INFO] ===== Completeness check finished =====
[2023-03-15 03:39:26,134] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:39:26,134] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37852/markers.fasta)
[2023-03-15 03:39:26,136] [INFO] Task started: Blastn
[2023-03-15 03:39:26,136] [INFO] Running command: blastn -query OceanDNA-b37852/markers.fasta -db /var/lib/cwl/stgdd2e05d3-9c6c-4f89-ab49-d687376ca142/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37852/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:39:26,945] [INFO] Task succeeded: Blastn
[2023-03-15 03:39:26,946] [INFO] Selected 12 target genomes.
[2023-03-15 03:39:26,946] [INFO] Target genome list was writen to OceanDNA-b37852/target_genomes_gtdb.txt
[2023-03-15 03:39:27,023] [INFO] Task started: fastANI
[2023-03-15 03:39:27,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg52745dec-0f4b-4da4-85d7-e7bb9046c5db/OceanDNA-b37852.fa --refList OceanDNA-b37852/target_genomes_gtdb.txt --output OceanDNA-b37852/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:39:32,092] [INFO] Task succeeded: fastANI
[2023-03-15 03:39:32,099] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:39:32,099] [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_002377985.1	s__Luminiphilus sp002377985	78.3917	178	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779445.1	s__Luminiphilus sp016779445	78.216	155	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.89	98.12	0.82	0.77	3	-
GCA_008081075.1	s__Luminiphilus sp008081075	77.669	121	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683335.1	s__Luminiphilus sp002683335	77.379	142	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.43	98.43	0.60	0.60	2	-
GCA_902623175.1	s__Luminiphilus sp902623175	77.2461	66	468	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	76.9262	59	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778045.1	s__Luminiphilus sp016778045	76.8758	52	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	76.7725	61	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683395.1	s__Luminiphilus sp002683395	76.5761	66	468	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:39:32,100] [INFO] GTDB search result was written to OceanDNA-b37852/result_gtdb.tsv
[2023-03-15 03:39:32,102] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:39:32,104] [INFO] DFAST_QC result json was written to OceanDNA-b37852/dqc_result.json
[2023-03-15 03:39:32,104] [INFO] DFAST_QC completed!
[2023-03-15 03:39:32,104] [INFO] Total running time: 0h0m57s