[2023-03-14 11:14:12,736] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,736] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference
[2023-03-14 11:14:14,214] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,215] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,215] [INFO] Running command: cat /var/lib/cwl/stgd2b673e9-9b1f-48cc-a23e-7d6d386e3cd8/OceanDNA-b12612.fa | prodigal -d OceanDNA-b12612/cds.fna -a OceanDNA-b12612/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:20,690] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:20,690] [INFO] Task started: HMMsearch
[2023-03-14 11:14:20,690] [INFO] Running command: hmmsearch --tblout OceanDNA-b12612/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference/reference_markers.hmm OceanDNA-b12612/protein.faa > /dev/null
[2023-03-14 11:14:20,851] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:20,852] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd2b673e9-9b1f-48cc-a23e-7d6d386e3cd8/OceanDNA-b12612.fa]
[2023-03-14 11:14:20,865] [INFO] Query marker FASTA was written to OceanDNA-b12612/markers.fasta
[2023-03-14 11:14:20,867] [INFO] Task started: Blastn
[2023-03-14 11:14:20,867] [INFO] Running command: blastn -query OceanDNA-b12612/markers.fasta -db /var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference/reference_markers.fasta -out OceanDNA-b12612/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:21,322] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:21,323] [INFO] Selected 10 target genomes.
[2023-03-14 11:14:21,323] [INFO] Target genome list was writen to OceanDNA-b12612/target_genomes.txt
[2023-03-14 11:14:21,331] [INFO] Task started: fastANI
[2023-03-14 11:14:21,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2b673e9-9b1f-48cc-a23e-7d6d386e3cd8/OceanDNA-b12612.fa --refList OceanDNA-b12612/target_genomes.txt --output OceanDNA-b12612/fastani_result.tsv --threads 1
[2023-03-14 11:14:27,107] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:27,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:27,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:27,108] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:27,108] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:27,108] [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 11:14:27,109] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12612/tc_result.tsv
[2023-03-14 11:14:27,109] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:27,109] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:27,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference/checkm_data
[2023-03-14 11:14:27,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:27,115] [INFO] Task started: CheckM
[2023-03-14 11:14:27,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12612/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12612/checkm_input OceanDNA-b12612/checkm_result
[2023-03-14 11:14:50,109] [INFO] Task succeeded: CheckM
[2023-03-14 11:14:50,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.85%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:14:50,111] [INFO] ===== Completeness check finished =====
[2023-03-14 11:14:50,111] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:14:50,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12612/markers.fasta)
[2023-03-14 11:14:50,113] [INFO] Task started: Blastn
[2023-03-14 11:14:50,113] [INFO] Running command: blastn -query OceanDNA-b12612/markers.fasta -db /var/lib/cwl/stgdd724c39-ad7b-4bf2-bc01-b48949dd4fbd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12612/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:50,664] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:50,665] [INFO] Selected 10 target genomes.
[2023-03-14 11:14:50,665] [INFO] Target genome list was writen to OceanDNA-b12612/target_genomes_gtdb.txt
[2023-03-14 11:14:50,678] [INFO] Task started: fastANI
[2023-03-14 11:14:50,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2b673e9-9b1f-48cc-a23e-7d6d386e3cd8/OceanDNA-b12612.fa --refList OceanDNA-b12612/target_genomes_gtdb.txt --output OceanDNA-b12612/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:14:57,026] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:57,029] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:14:57,029] [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_016183805.1	s__Vicingus sp016183805	78.627	59	116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075325.1	s__Vicingus sp015075325	78.2745	62	116	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	96.71	96.71	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:14:57,029] [INFO] GTDB search result was written to OceanDNA-b12612/result_gtdb.tsv
[2023-03-14 11:14:57,029] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:14:57,030] [INFO] DFAST_QC result json was written to OceanDNA-b12612/dqc_result.json
[2023-03-14 11:14:57,030] [INFO] DFAST_QC completed!
[2023-03-14 11:14:57,030] [INFO] Total running time: 0h0m44s