[2023-03-16 23:35:12,983] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,984] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,984] [INFO] DQC Reference Directory: /var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference
[2023-03-16 23:35:14,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stgdeba36df-7439-4a7b-8fdc-816bda5fbaa9/OceanDNA-b18620.fa | prodigal -d OceanDNA-b18620/cds.fna -a OceanDNA-b18620/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:22,118] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:22,118] [INFO] Task started: HMMsearch
[2023-03-16 23:35:22,118] [INFO] Running command: hmmsearch --tblout OceanDNA-b18620/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference/reference_markers.hmm OceanDNA-b18620/protein.faa > /dev/null
[2023-03-16 23:35:22,285] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:22,286] [INFO] Found 6/6 markers.
[2023-03-16 23:35:22,300] [INFO] Query marker FASTA was written to OceanDNA-b18620/markers.fasta
[2023-03-16 23:35:22,300] [INFO] Task started: Blastn
[2023-03-16 23:35:22,300] [INFO] Running command: blastn -query OceanDNA-b18620/markers.fasta -db /var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference/reference_markers.fasta -out OceanDNA-b18620/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:22,798] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:22,799] [INFO] Selected 19 target genomes.
[2023-03-16 23:35:22,799] [INFO] Target genome list was writen to OceanDNA-b18620/target_genomes.txt
[2023-03-16 23:35:22,811] [INFO] Task started: fastANI
[2023-03-16 23:35:22,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeba36df-7439-4a7b-8fdc-816bda5fbaa9/OceanDNA-b18620.fa --refList OceanDNA-b18620/target_genomes.txt --output OceanDNA-b18620/fastani_result.tsv --threads 1
[2023-03-16 23:35:33,762] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:33,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:33,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:33,763] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:33,763] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:33,763] [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
--------------------------------------------------------------------------------
[2023-03-16 23:35:33,763] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18620/tc_result.tsv
[2023-03-16 23:35:33,764] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:33,764] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:33,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference/checkm_data
[2023-03-16 23:35:33,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:33,769] [INFO] Task started: CheckM
[2023-03-16 23:35:33,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18620/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18620/checkm_input OceanDNA-b18620/checkm_result
[2023-03-16 23:35:58,807] [INFO] Task succeeded: CheckM
[2023-03-16 23:35:58,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.69%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:35:58,810] [INFO] ===== Completeness check finished =====
[2023-03-16 23:35:58,810] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:35:58,810] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18620/markers.fasta)
[2023-03-16 23:35:58,810] [INFO] Task started: Blastn
[2023-03-16 23:35:58,810] [INFO] Running command: blastn -query OceanDNA-b18620/markers.fasta -db /var/lib/cwl/stgd02a35a7-d21b-4333-91e3-0d7ff8bf41dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18620/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:59,520] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:59,521] [INFO] Selected 22 target genomes.
[2023-03-16 23:35:59,521] [INFO] Target genome list was writen to OceanDNA-b18620/target_genomes_gtdb.txt
[2023-03-16 23:35:59,976] [INFO] Task started: fastANI
[2023-03-16 23:35:59,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeba36df-7439-4a7b-8fdc-816bda5fbaa9/OceanDNA-b18620.fa --refList OceanDNA-b18620/target_genomes_gtdb.txt --output OceanDNA-b18620/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:07,710] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:07,713] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:36:07,713] [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_002701785.1	s__GCA-002701945 sp002701785	82.7871	380	502	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	97.49	97.49	0.87	0.87	2	-
GCA_004321715.1	s__GCA-002701945 sp004321715	81.7719	299	502	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701945.1	s__GCA-002701945 sp002701945	80.5151	280	502	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964215.1	s__GCA-002701945 sp012964215	76.2254	52	502	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__GCA-002701945	95.0	98.56	98.56	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:07,713] [INFO] GTDB search result was written to OceanDNA-b18620/result_gtdb.tsv
[2023-03-16 23:36:07,713] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:07,714] [INFO] DFAST_QC result json was written to OceanDNA-b18620/dqc_result.json
[2023-03-16 23:36:07,714] [INFO] DFAST_QC completed!
[2023-03-16 23:36:07,714] [INFO] Total running time: 0h0m55s