[2023-03-19 02:29:22,732] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:29:22,733] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:29:22,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference
[2023-03-19 02:29:23,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:29:23,837] [INFO] Task started: Prodigal
[2023-03-19 02:29:23,837] [INFO] Running command: cat /var/lib/cwl/stgad243aa7-72e4-4464-90c0-b4973ec6bdd5/OceanDNA-b3584.fa | prodigal -d OceanDNA-b3584/cds.fna -a OceanDNA-b3584/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:29:47,062] [INFO] Task succeeded: Prodigal
[2023-03-19 02:29:47,062] [INFO] Task started: HMMsearch
[2023-03-19 02:29:47,062] [INFO] Running command: hmmsearch --tblout OceanDNA-b3584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference/reference_markers.hmm OceanDNA-b3584/protein.faa > /dev/null
[2023-03-19 02:29:47,269] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:29:47,270] [INFO] Found 6/6 markers.
[2023-03-19 02:29:47,296] [INFO] Query marker FASTA was written to OceanDNA-b3584/markers.fasta
[2023-03-19 02:29:47,297] [INFO] Task started: Blastn
[2023-03-19 02:29:47,298] [INFO] Running command: blastn -query OceanDNA-b3584/markers.fasta -db /var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference/reference_markers.fasta -out OceanDNA-b3584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:29:47,841] [INFO] Task succeeded: Blastn
[2023-03-19 02:29:47,844] [INFO] Selected 32 target genomes.
[2023-03-19 02:29:47,844] [INFO] Target genome list was writen to OceanDNA-b3584/target_genomes.txt
[2023-03-19 02:29:47,863] [INFO] Task started: fastANI
[2023-03-19 02:29:47,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgad243aa7-72e4-4464-90c0-b4973ec6bdd5/OceanDNA-b3584.fa --refList OceanDNA-b3584/target_genomes.txt --output OceanDNA-b3584/fastani_result.tsv --threads 1
[2023-03-19 02:30:17,888] [INFO] Task succeeded: fastANI
[2023-03-19 02:30:17,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:30:17,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:30:17,889] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:30:17,889] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:30:17,889] [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
--------------------------------------------------------------------------------
[2023-03-19 02:30:17,890] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3584/tc_result.tsv
[2023-03-19 02:30:17,890] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:30:17,890] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:30:17,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference/checkm_data
[2023-03-19 02:30:17,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:30:17,899] [INFO] Task started: CheckM
[2023-03-19 02:30:17,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3584/checkm_input OceanDNA-b3584/checkm_result
[2023-03-19 02:31:20,021] [INFO] Task succeeded: CheckM
[2023-03-19 02:31:20,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.31%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:31:20,024] [INFO] ===== Completeness check finished =====
[2023-03-19 02:31:20,024] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:31:20,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3584/markers.fasta)
[2023-03-19 02:31:20,025] [INFO] Task started: Blastn
[2023-03-19 02:31:20,025] [INFO] Running command: blastn -query OceanDNA-b3584/markers.fasta -db /var/lib/cwl/stgdd694cb2-9ae4-41f6-86aa-a0e96032f167/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:31:20,784] [INFO] Task succeeded: Blastn
[2023-03-19 02:31:20,785] [INFO] Selected 35 target genomes.
[2023-03-19 02:31:20,785] [INFO] Target genome list was writen to OceanDNA-b3584/target_genomes_gtdb.txt
[2023-03-19 02:31:20,836] [INFO] Task started: fastANI
[2023-03-19 02:31:20,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgad243aa7-72e4-4464-90c0-b4973ec6bdd5/OceanDNA-b3584.fa --refList OceanDNA-b3584/target_genomes_gtdb.txt --output OceanDNA-b3584/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:31:46,878] [INFO] Task succeeded: fastANI
[2023-03-19 02:31:46,879] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:31:46,879] [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
--------------------------------------------------------------------------------
[2023-03-19 02:31:46,879] [INFO] GTDB search result was written to OceanDNA-b3584/result_gtdb.tsv
[2023-03-19 02:31:46,879] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:31:46,880] [INFO] DFAST_QC result json was written to OceanDNA-b3584/dqc_result.json
[2023-03-19 02:31:46,880] [INFO] DFAST_QC completed!
[2023-03-19 02:31:46,880] [INFO] Total running time: 0h2m24s