[2023-03-17 08:31:46,166] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:31:46,166] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:31:46,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference
[2023-03-17 08:31:47,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:31:47,408] [INFO] Task started: Prodigal
[2023-03-17 08:31:47,409] [INFO] Running command: cat /var/lib/cwl/stg962c9e96-c1b0-4cb7-bb8d-0f6fce699405/OceanDNA-b22094.fa | prodigal -d OceanDNA-b22094/cds.fna -a OceanDNA-b22094/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:32:07,189] [INFO] Task succeeded: Prodigal
[2023-03-17 08:32:07,190] [INFO] Task started: HMMsearch
[2023-03-17 08:32:07,190] [INFO] Running command: hmmsearch --tblout OceanDNA-b22094/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference/reference_markers.hmm OceanDNA-b22094/protein.faa > /dev/null
[2023-03-17 08:32:07,393] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:32:07,394] [INFO] Found 6/6 markers.
[2023-03-17 08:32:07,413] [INFO] Query marker FASTA was written to OceanDNA-b22094/markers.fasta
[2023-03-17 08:32:07,414] [INFO] Task started: Blastn
[2023-03-17 08:32:07,414] [INFO] Running command: blastn -query OceanDNA-b22094/markers.fasta -db /var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference/reference_markers.fasta -out OceanDNA-b22094/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:32:07,920] [INFO] Task succeeded: Blastn
[2023-03-17 08:32:07,921] [INFO] Selected 15 target genomes.
[2023-03-17 08:32:07,921] [INFO] Target genome list was writen to OceanDNA-b22094/target_genomes.txt
[2023-03-17 08:32:08,185] [INFO] Task started: fastANI
[2023-03-17 08:32:08,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg962c9e96-c1b0-4cb7-bb8d-0f6fce699405/OceanDNA-b22094.fa --refList OceanDNA-b22094/target_genomes.txt --output OceanDNA-b22094/fastani_result.tsv --threads 1
[2023-03-17 08:32:15,875] [INFO] Task succeeded: fastANI
[2023-03-17 08:32:15,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:32:15,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:32:15,876] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:32:15,876] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:32:15,876] [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
--------------------------------------------------------------------------------
[2023-03-17 08:32:15,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22094/tc_result.tsv
[2023-03-17 08:32:15,876] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:32:15,876] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:32:15,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference/checkm_data
[2023-03-17 08:32:15,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:32:15,991] [INFO] Task started: CheckM
[2023-03-17 08:32:15,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22094/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22094/checkm_input OceanDNA-b22094/checkm_result
[2023-03-17 08:33:07,252] [INFO] Task succeeded: CheckM
[2023-03-17 08:33:07,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:33:07,255] [INFO] ===== Completeness check finished =====
[2023-03-17 08:33:07,255] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:33:07,255] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22094/markers.fasta)
[2023-03-17 08:33:07,256] [INFO] Task started: Blastn
[2023-03-17 08:33:07,256] [INFO] Running command: blastn -query OceanDNA-b22094/markers.fasta -db /var/lib/cwl/stgeec7b13e-0654-41da-bacd-929e599453d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22094/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:33:07,958] [INFO] Task succeeded: Blastn
[2023-03-17 08:33:07,959] [INFO] Selected 25 target genomes.
[2023-03-17 08:33:07,959] [INFO] Target genome list was writen to OceanDNA-b22094/target_genomes_gtdb.txt
[2023-03-17 08:33:08,864] [INFO] Task started: fastANI
[2023-03-17 08:33:08,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg962c9e96-c1b0-4cb7-bb8d-0f6fce699405/OceanDNA-b22094.fa --refList OceanDNA-b22094/target_genomes_gtdb.txt --output OceanDNA-b22094/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:33:20,950] [INFO] Task succeeded: fastANI
[2023-03-17 08:33:20,952] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:33:20,953] [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_002716625.1	s__UBA6626 sp002716625	99.8431	945	1044	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__UBA6626	95.0	99.72	99.72	0.87	0.87	2	conclusive
--------------------------------------------------------------------------------
[2023-03-17 08:33:20,953] [INFO] GTDB search result was written to OceanDNA-b22094/result_gtdb.tsv
[2023-03-17 08:33:20,953] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:33:20,953] [INFO] DFAST_QC result json was written to OceanDNA-b22094/dqc_result.json
[2023-03-17 08:33:20,953] [INFO] DFAST_QC completed!
[2023-03-17 08:33:20,953] [INFO] Total running time: 0h1m35s