[2023-03-18 22:39:28,804] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:39:28,804] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:39:28,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference
[2023-03-18 22:39:29,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:39:29,939] [INFO] Task started: Prodigal
[2023-03-18 22:39:29,939] [INFO] Running command: cat /var/lib/cwl/stgc7ba89fc-87b6-419c-9eda-a9558518367d/OceanDNA-b22284.fa | prodigal -d OceanDNA-b22284/cds.fna -a OceanDNA-b22284/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:39:34,884] [INFO] Task succeeded: Prodigal
[2023-03-18 22:39:34,884] [INFO] Task started: HMMsearch
[2023-03-18 22:39:34,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b22284/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference/reference_markers.hmm OceanDNA-b22284/protein.faa > /dev/null
[2023-03-18 22:39:35,027] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:39:35,028] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc7ba89fc-87b6-419c-9eda-a9558518367d/OceanDNA-b22284.fa]
[2023-03-18 22:39:35,039] [INFO] Query marker FASTA was written to OceanDNA-b22284/markers.fasta
[2023-03-18 22:39:35,041] [INFO] Task started: Blastn
[2023-03-18 22:39:35,041] [INFO] Running command: blastn -query OceanDNA-b22284/markers.fasta -db /var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference/reference_markers.fasta -out OceanDNA-b22284/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:39:35,587] [INFO] Task succeeded: Blastn
[2023-03-18 22:39:35,587] [INFO] Selected 25 target genomes.
[2023-03-18 22:39:35,588] [INFO] Target genome list was writen to OceanDNA-b22284/target_genomes.txt
[2023-03-18 22:39:35,623] [INFO] Task started: fastANI
[2023-03-18 22:39:35,623] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ba89fc-87b6-419c-9eda-a9558518367d/OceanDNA-b22284.fa --refList OceanDNA-b22284/target_genomes.txt --output OceanDNA-b22284/fastani_result.tsv --threads 1
[2023-03-18 22:39:54,493] [INFO] Task succeeded: fastANI
[2023-03-18 22:39:54,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:39:54,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:39:54,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:39:54,494] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:39:54,494] [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
--------------------------------------------------------------------------------
[2023-03-18 22:39:54,494] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22284/tc_result.tsv
[2023-03-18 22:39:54,494] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:39:54,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:39:54,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference/checkm_data
[2023-03-18 22:39:54,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:39:54,500] [INFO] Task started: CheckM
[2023-03-18 22:39:54,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22284/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22284/checkm_input OceanDNA-b22284/checkm_result
[2023-03-18 22:40:13,161] [INFO] Task succeeded: CheckM
[2023-03-18 22:40:13,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.67%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:40:13,164] [INFO] ===== Completeness check finished =====
[2023-03-18 22:40:13,164] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:40:13,164] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22284/markers.fasta)
[2023-03-18 22:40:13,165] [INFO] Task started: Blastn
[2023-03-18 22:40:13,165] [INFO] Running command: blastn -query OceanDNA-b22284/markers.fasta -db /var/lib/cwl/stgfdb2913c-71cb-4b30-a855-7b16be2f0ae3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22284/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:40:13,830] [INFO] Task succeeded: Blastn
[2023-03-18 22:40:13,830] [INFO] Selected 11 target genomes.
[2023-03-18 22:40:13,830] [INFO] Target genome list was writen to OceanDNA-b22284/target_genomes_gtdb.txt
[2023-03-18 22:40:13,839] [INFO] Task started: fastANI
[2023-03-18 22:40:13,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7ba89fc-87b6-419c-9eda-a9558518367d/OceanDNA-b22284.fa --refList OceanDNA-b22284/target_genomes_gtdb.txt --output OceanDNA-b22284/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:40:17,539] [INFO] Task succeeded: fastANI
[2023-03-18 22:40:17,542] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:40:17,542] [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_002705085.1	s__UBA8653 sp002705085	99.1054	71	73	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002168105.2	s__UBA8653 sp002168105	83.6708	52	73	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	99.39	99.39	0.92	0.92	2	-
GCA_004213555.1	s__UBA8653 sp002862275	82.5559	50	73	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8653	95.0	98.78	97.23	0.90	0.87	4	-
--------------------------------------------------------------------------------
[2023-03-18 22:40:17,543] [INFO] GTDB search result was written to OceanDNA-b22284/result_gtdb.tsv
[2023-03-18 22:40:17,543] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:40:17,543] [INFO] DFAST_QC result json was written to OceanDNA-b22284/dqc_result.json
[2023-03-18 22:40:17,543] [INFO] DFAST_QC completed!
[2023-03-18 22:40:17,543] [INFO] Total running time: 0h0m49s