[2023-03-18 23:31:26,231] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:31:26,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:31:26,232] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference
[2023-03-18 23:31:27,397] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:31:27,397] [INFO] Task started: Prodigal
[2023-03-18 23:31:27,397] [INFO] Running command: cat /var/lib/cwl/stg523501ed-923e-44d4-be5e-dd01efbbf206/OceanDNA-b31314.fa | prodigal -d OceanDNA-b31314/cds.fna -a OceanDNA-b31314/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:31:37,373] [INFO] Task succeeded: Prodigal
[2023-03-18 23:31:37,373] [INFO] Task started: HMMsearch
[2023-03-18 23:31:37,373] [INFO] Running command: hmmsearch --tblout OceanDNA-b31314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference/reference_markers.hmm OceanDNA-b31314/protein.faa > /dev/null
[2023-03-18 23:31:37,540] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:31:37,541] [INFO] Found 6/6 markers.
[2023-03-18 23:31:37,556] [INFO] Query marker FASTA was written to OceanDNA-b31314/markers.fasta
[2023-03-18 23:31:37,557] [INFO] Task started: Blastn
[2023-03-18 23:31:37,557] [INFO] Running command: blastn -query OceanDNA-b31314/markers.fasta -db /var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference/reference_markers.fasta -out OceanDNA-b31314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:31:38,122] [INFO] Task succeeded: Blastn
[2023-03-18 23:31:38,124] [INFO] Selected 23 target genomes.
[2023-03-18 23:31:38,124] [INFO] Target genome list was writen to OceanDNA-b31314/target_genomes.txt
[2023-03-18 23:31:38,136] [INFO] Task started: fastANI
[2023-03-18 23:31:38,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg523501ed-923e-44d4-be5e-dd01efbbf206/OceanDNA-b31314.fa --refList OceanDNA-b31314/target_genomes.txt --output OceanDNA-b31314/fastani_result.tsv --threads 1
[2023-03-18 23:31:49,854] [INFO] Task succeeded: fastANI
[2023-03-18 23:31:49,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:31:49,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:31:49,854] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:31:49,855] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:31:49,855] [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 23:31:49,855] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31314/tc_result.tsv
[2023-03-18 23:31:49,855] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:31:49,855] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:31:49,855] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference/checkm_data
[2023-03-18 23:31:49,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:31:50,062] [INFO] Task started: CheckM
[2023-03-18 23:31:50,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31314/checkm_input OceanDNA-b31314/checkm_result
[2023-03-18 23:32:19,237] [INFO] Task succeeded: CheckM
[2023-03-18 23:32:19,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.34%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:32:19,240] [INFO] ===== Completeness check finished =====
[2023-03-18 23:32:19,240] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:32:19,240] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31314/markers.fasta)
[2023-03-18 23:32:19,242] [INFO] Task started: Blastn
[2023-03-18 23:32:19,242] [INFO] Running command: blastn -query OceanDNA-b31314/markers.fasta -db /var/lib/cwl/stgc9f53807-3bbe-4b4d-806d-6bd4902298da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:32:20,138] [INFO] Task succeeded: Blastn
[2023-03-18 23:32:20,139] [INFO] Selected 25 target genomes.
[2023-03-18 23:32:20,139] [INFO] Target genome list was writen to OceanDNA-b31314/target_genomes_gtdb.txt
[2023-03-18 23:32:20,158] [INFO] Task started: fastANI
[2023-03-18 23:32:20,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg523501ed-923e-44d4-be5e-dd01efbbf206/OceanDNA-b31314.fa --refList OceanDNA-b31314/target_genomes_gtdb.txt --output OceanDNA-b31314/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:32:30,013] [INFO] Task succeeded: fastANI
[2023-03-18 23:32:30,015] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:32:30,015] [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_002712165.1	s__UBA11612 sp002712165	99.6949	548	593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__UBA11612	95.0	99.52	99.52	0.89	0.89	2	conclusive
--------------------------------------------------------------------------------
[2023-03-18 23:32:30,015] [INFO] GTDB search result was written to OceanDNA-b31314/result_gtdb.tsv
[2023-03-18 23:32:30,015] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:32:30,016] [INFO] DFAST_QC result json was written to OceanDNA-b31314/dqc_result.json
[2023-03-18 23:32:30,016] [INFO] DFAST_QC completed!
[2023-03-18 23:32:30,016] [INFO] Total running time: 0h1m4s