[2023-03-17 04:15:16,780] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:16,780] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:16,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference
[2023-03-17 04:15:17,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:17,949] [INFO] Task started: Prodigal
[2023-03-17 04:15:17,949] [INFO] Running command: cat /var/lib/cwl/stg88015c25-e836-4f0a-857d-996a5d2f8258/OceanDNA-a3149.fa | prodigal -d OceanDNA-a3149/cds.fna -a OceanDNA-a3149/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:23,673] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:23,673] [INFO] Task started: HMMsearch
[2023-03-17 04:15:23,673] [INFO] Running command: hmmsearch --tblout OceanDNA-a3149/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference/reference_markers.hmm OceanDNA-a3149/protein.faa > /dev/null
[2023-03-17 04:15:23,816] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:23,816] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg88015c25-e836-4f0a-857d-996a5d2f8258/OceanDNA-a3149.fa]
[2023-03-17 04:15:23,826] [INFO] Query marker FASTA was written to OceanDNA-a3149/markers.fasta
[2023-03-17 04:15:23,826] [INFO] Task started: Blastn
[2023-03-17 04:15:23,826] [INFO] Running command: blastn -query OceanDNA-a3149/markers.fasta -db /var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference/reference_markers.fasta -out OceanDNA-a3149/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:24,251] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:24,252] [INFO] Selected 5 target genomes.
[2023-03-17 04:15:24,252] [INFO] Target genome list was writen to OceanDNA-a3149/target_genomes.txt
[2023-03-17 04:15:24,255] [INFO] Task started: fastANI
[2023-03-17 04:15:24,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg88015c25-e836-4f0a-857d-996a5d2f8258/OceanDNA-a3149.fa --refList OceanDNA-a3149/target_genomes.txt --output OceanDNA-a3149/fastani_result.tsv --threads 1
[2023-03-17 04:15:26,549] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:26,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:26,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:26,550] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:26,550] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:15:26,550] [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 04:15:26,550] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3149/tc_result.tsv
[2023-03-17 04:15:26,550] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:26,550] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:26,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference/checkm_data
[2023-03-17 04:15:26,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:26,556] [INFO] Task started: CheckM
[2023-03-17 04:15:26,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3149/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3149/checkm_input OceanDNA-a3149/checkm_result
[2023-03-17 04:15:47,238] [INFO] Task succeeded: CheckM
[2023-03-17 04:15:47,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:15:47,241] [INFO] ===== Completeness check finished =====
[2023-03-17 04:15:47,241] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:15:47,241] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3149/markers.fasta)
[2023-03-17 04:15:47,241] [INFO] Task started: Blastn
[2023-03-17 04:15:47,241] [INFO] Running command: blastn -query OceanDNA-a3149/markers.fasta -db /var/lib/cwl/stg60e68572-1bf1-46a5-9ff3-de5eca489e4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3149/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:47,654] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:47,655] [INFO] Selected 6 target genomes.
[2023-03-17 04:15:47,655] [INFO] Target genome list was writen to OceanDNA-a3149/target_genomes_gtdb.txt
[2023-03-17 04:15:47,804] [INFO] Task started: fastANI
[2023-03-17 04:15:47,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg88015c25-e836-4f0a-857d-996a5d2f8258/OceanDNA-a3149.fa --refList OceanDNA-a3149/target_genomes_gtdb.txt --output OceanDNA-a3149/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:15:49,530] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:49,533] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:15:49,533] [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_012959275.1	s__UBA226 sp012959275	95.3627	270	307	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__UBA226	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014240385.1	s__UBA226 sp014240385	90.0403	197	307	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__UBA226	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:15:49,533] [INFO] GTDB search result was written to OceanDNA-a3149/result_gtdb.tsv
[2023-03-17 04:15:49,533] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:15:49,534] [INFO] DFAST_QC result json was written to OceanDNA-a3149/dqc_result.json
[2023-03-17 04:15:49,534] [INFO] DFAST_QC completed!
[2023-03-17 04:15:49,534] [INFO] Total running time: 0h0m33s