[2023-03-19 04:29:37,812] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,812] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference
[2023-03-19 04:29:38,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,916] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,916] [INFO] Running command: cat /var/lib/cwl/stga5e72d9b-c72d-4f57-b8a0-6a9d6ac10338/OceanDNA-b15473.fa | prodigal -d OceanDNA-b15473/cds.fna -a OceanDNA-b15473/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:47,594] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:47,594] [INFO] Task started: HMMsearch
[2023-03-19 04:29:47,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b15473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference/reference_markers.hmm OceanDNA-b15473/protein.faa > /dev/null
[2023-03-19 04:29:47,746] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:47,746] [INFO] Found 6/6 markers.
[2023-03-19 04:29:47,761] [INFO] Query marker FASTA was written to OceanDNA-b15473/markers.fasta
[2023-03-19 04:29:47,761] [INFO] Task started: Blastn
[2023-03-19 04:29:47,761] [INFO] Running command: blastn -query OceanDNA-b15473/markers.fasta -db /var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference/reference_markers.fasta -out OceanDNA-b15473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:48,271] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:48,272] [INFO] Selected 10 target genomes.
[2023-03-19 04:29:48,272] [INFO] Target genome list was writen to OceanDNA-b15473/target_genomes.txt
[2023-03-19 04:29:48,277] [INFO] Task started: fastANI
[2023-03-19 04:29:48,277] [INFO] Running command: fastANI --query /var/lib/cwl/stga5e72d9b-c72d-4f57-b8a0-6a9d6ac10338/OceanDNA-b15473.fa --refList OceanDNA-b15473/target_genomes.txt --output OceanDNA-b15473/fastani_result.tsv --threads 1
[2023-03-19 04:29:51,404] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:51,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:51,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:51,405] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:51,405] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:29:51,405] [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 04:29:51,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15473/tc_result.tsv
[2023-03-19 04:29:51,405] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:51,405] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:51,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference/checkm_data
[2023-03-19 04:29:51,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:51,411] [INFO] Task started: CheckM
[2023-03-19 04:29:51,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15473/checkm_input OceanDNA-b15473/checkm_result
[2023-03-19 04:30:17,968] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:17,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:17,970] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:17,970] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:17,971] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15473/markers.fasta)
[2023-03-19 04:30:17,971] [INFO] Task started: Blastn
[2023-03-19 04:30:17,971] [INFO] Running command: blastn -query OceanDNA-b15473/markers.fasta -db /var/lib/cwl/stg028df4c9-fc56-40e8-af4e-86137145d48f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:18,707] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:18,708] [INFO] Selected 14 target genomes.
[2023-03-19 04:30:18,708] [INFO] Target genome list was writen to OceanDNA-b15473/target_genomes_gtdb.txt
[2023-03-19 04:30:18,722] [INFO] Task started: fastANI
[2023-03-19 04:30:18,722] [INFO] Running command: fastANI --query /var/lib/cwl/stga5e72d9b-c72d-4f57-b8a0-6a9d6ac10338/OceanDNA-b15473.fa --refList OceanDNA-b15473/target_genomes_gtdb.txt --output OceanDNA-b15473/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:23,253] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:23,255] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:23,255] [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_002707185.1	s__GCA-2707185 sp002707185	78.9174	221	513	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__GCA-2707185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:23,255] [INFO] GTDB search result was written to OceanDNA-b15473/result_gtdb.tsv
[2023-03-19 04:30:23,255] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:23,256] [INFO] DFAST_QC result json was written to OceanDNA-b15473/dqc_result.json
[2023-03-19 04:30:23,256] [INFO] DFAST_QC completed!
[2023-03-19 04:30:23,256] [INFO] Total running time: 0h0m45s