[2023-03-16 18:27:22,317] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:27:22,318] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:27:22,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference
[2023-03-16 18:27:24,843] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:27:24,843] [INFO] Task started: Prodigal
[2023-03-16 18:27:24,843] [INFO] Running command: cat /var/lib/cwl/stg95d4914c-8e4c-4ca9-8491-c0fc9fb33348/OceanDNA-b5175.fa | prodigal -d OceanDNA-b5175/cds.fna -a OceanDNA-b5175/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:27:32,532] [INFO] Task succeeded: Prodigal
[2023-03-16 18:27:32,532] [INFO] Task started: HMMsearch
[2023-03-16 18:27:32,532] [INFO] Running command: hmmsearch --tblout OceanDNA-b5175/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference/reference_markers.hmm OceanDNA-b5175/protein.faa > /dev/null
[2023-03-16 18:27:32,690] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:27:32,691] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg95d4914c-8e4c-4ca9-8491-c0fc9fb33348/OceanDNA-b5175.fa]
[2023-03-16 18:27:32,701] [INFO] Query marker FASTA was written to OceanDNA-b5175/markers.fasta
[2023-03-16 18:27:32,701] [INFO] Task started: Blastn
[2023-03-16 18:27:32,701] [INFO] Running command: blastn -query OceanDNA-b5175/markers.fasta -db /var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference/reference_markers.fasta -out OceanDNA-b5175/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:27:33,200] [INFO] Task succeeded: Blastn
[2023-03-16 18:27:33,201] [INFO] Selected 20 target genomes.
[2023-03-16 18:27:33,202] [INFO] Target genome list was writen to OceanDNA-b5175/target_genomes.txt
[2023-03-16 18:27:33,210] [INFO] Task started: fastANI
[2023-03-16 18:27:33,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d4914c-8e4c-4ca9-8491-c0fc9fb33348/OceanDNA-b5175.fa --refList OceanDNA-b5175/target_genomes.txt --output OceanDNA-b5175/fastani_result.tsv --threads 1
[2023-03-16 18:27:44,246] [INFO] Task succeeded: fastANI
[2023-03-16 18:27:44,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:27:44,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:27:44,247] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:27:44,247] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:27:44,247] [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 18:27:44,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5175/tc_result.tsv
[2023-03-16 18:27:44,247] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:27:44,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:27:44,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference/checkm_data
[2023-03-16 18:27:44,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:27:44,253] [INFO] Task started: CheckM
[2023-03-16 18:27:44,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5175/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5175/checkm_input OceanDNA-b5175/checkm_result
[2023-03-16 18:28:12,595] [INFO] Task succeeded: CheckM
[2023-03-16 18:28:12,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.15%
Contamintation: 4.69%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:28:12,598] [INFO] ===== Completeness check finished =====
[2023-03-16 18:28:12,598] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:28:12,598] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5175/markers.fasta)
[2023-03-16 18:28:12,598] [INFO] Task started: Blastn
[2023-03-16 18:28:12,598] [INFO] Running command: blastn -query OceanDNA-b5175/markers.fasta -db /var/lib/cwl/stgb05c1b3e-846b-4f92-b9f0-131bb4982a52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5175/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:28:13,210] [INFO] Task succeeded: Blastn
[2023-03-16 18:28:13,211] [INFO] Selected 17 target genomes.
[2023-03-16 18:28:13,211] [INFO] Target genome list was writen to OceanDNA-b5175/target_genomes_gtdb.txt
[2023-03-16 18:28:13,228] [INFO] Task started: fastANI
[2023-03-16 18:28:13,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg95d4914c-8e4c-4ca9-8491-c0fc9fb33348/OceanDNA-b5175.fa --refList OceanDNA-b5175/target_genomes_gtdb.txt --output OceanDNA-b5175/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:28:19,777] [INFO] Task succeeded: fastANI
[2023-03-16 18:28:19,780] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:28:19,781] [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_002862585.1	s__GCA-2862585 sp002862585	90.2961	128	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779935.1	s__GCA-2862585 sp016779935	84.8683	175	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	99.89	99.89	0.93	0.93	2	-
GCA_016779995.1	s__UBA8444 sp016779995	76.8824	72	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA8444	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:28:19,781] [INFO] GTDB search result was written to OceanDNA-b5175/result_gtdb.tsv
[2023-03-16 18:28:19,781] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:28:19,782] [INFO] DFAST_QC result json was written to OceanDNA-b5175/dqc_result.json
[2023-03-16 18:28:19,782] [INFO] DFAST_QC completed!
[2023-03-16 18:28:19,782] [INFO] Total running time: 0h0m57s