[2023-03-18 06:30:24,718] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,718] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference
[2023-03-18 06:30:25,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,871] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,872] [INFO] Running command: cat /var/lib/cwl/stg7767e5fa-6adb-44d4-bfbc-8a3bfbe199ed/OceanDNA-b45577.fa | prodigal -d OceanDNA-b45577/cds.fna -a OceanDNA-b45577/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:31,802] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:31,802] [INFO] Task started: HMMsearch
[2023-03-18 06:30:31,802] [INFO] Running command: hmmsearch --tblout OceanDNA-b45577/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference/reference_markers.hmm OceanDNA-b45577/protein.faa > /dev/null
[2023-03-18 06:30:31,930] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:31,931] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7767e5fa-6adb-44d4-bfbc-8a3bfbe199ed/OceanDNA-b45577.fa]
[2023-03-18 06:30:31,943] [INFO] Query marker FASTA was written to OceanDNA-b45577/markers.fasta
[2023-03-18 06:30:31,943] [INFO] Task started: Blastn
[2023-03-18 06:30:31,943] [INFO] Running command: blastn -query OceanDNA-b45577/markers.fasta -db /var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference/reference_markers.fasta -out OceanDNA-b45577/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:32,377] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:32,385] [INFO] Selected 12 target genomes.
[2023-03-18 06:30:32,386] [INFO] Target genome list was writen to OceanDNA-b45577/target_genomes.txt
[2023-03-18 06:30:32,472] [INFO] Task started: fastANI
[2023-03-18 06:30:32,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg7767e5fa-6adb-44d4-bfbc-8a3bfbe199ed/OceanDNA-b45577.fa --refList OceanDNA-b45577/target_genomes.txt --output OceanDNA-b45577/fastani_result.tsv --threads 1
[2023-03-18 06:30:39,598] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:39,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:39,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:39,599] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:39,599] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:30:39,599] [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 06:30:39,603] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45577/tc_result.tsv
[2023-03-18 06:30:39,605] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:39,605] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:39,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference/checkm_data
[2023-03-18 06:30:39,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:39,613] [INFO] Task started: CheckM
[2023-03-18 06:30:39,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45577/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45577/checkm_input OceanDNA-b45577/checkm_result
[2023-03-18 06:31:00,793] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:00,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:00,840] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:00,840] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:00,840] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45577/markers.fasta)
[2023-03-18 06:31:00,841] [INFO] Task started: Blastn
[2023-03-18 06:31:00,841] [INFO] Running command: blastn -query OceanDNA-b45577/markers.fasta -db /var/lib/cwl/stgc89941e7-3db7-46a3-9a19-bc7ceb0ee838/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45577/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:01,288] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:01,295] [INFO] Selected 19 target genomes.
[2023-03-18 06:31:01,295] [INFO] Target genome list was writen to OceanDNA-b45577/target_genomes_gtdb.txt
[2023-03-18 06:31:01,586] [INFO] Task started: fastANI
[2023-03-18 06:31:01,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg7767e5fa-6adb-44d4-bfbc-8a3bfbe199ed/OceanDNA-b45577.fa --refList OceanDNA-b45577/target_genomes_gtdb.txt --output OceanDNA-b45577/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:11,193] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:11,195] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:31:11,195] [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_018645725.1	s__MB11C04 sp018645725	79.1801	71	140	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:11,201] [INFO] GTDB search result was written to OceanDNA-b45577/result_gtdb.tsv
[2023-03-18 06:31:11,210] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:11,216] [INFO] DFAST_QC result json was written to OceanDNA-b45577/dqc_result.json
[2023-03-18 06:31:11,216] [INFO] DFAST_QC completed!
[2023-03-18 06:31:11,216] [INFO] Total running time: 0h0m46s