[2023-03-15 16:41:11,416] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:41:11,416] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:41:11,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference
[2023-03-15 16:41:13,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:41:13,952] [INFO] Task started: Prodigal
[2023-03-15 16:41:13,952] [INFO] Running command: cat /var/lib/cwl/stg9d3274c5-705a-4cd6-94fe-27e80672fa16/OceanDNA-a1308.fa | prodigal -d OceanDNA-a1308/cds.fna -a OceanDNA-a1308/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:41:18,443] [INFO] Task succeeded: Prodigal
[2023-03-15 16:41:18,443] [INFO] Task started: HMMsearch
[2023-03-15 16:41:18,443] [INFO] Running command: hmmsearch --tblout OceanDNA-a1308/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference/reference_markers.hmm OceanDNA-a1308/protein.faa > /dev/null
[2023-03-15 16:41:18,640] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:41:18,640] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9d3274c5-705a-4cd6-94fe-27e80672fa16/OceanDNA-a1308.fa]
[2023-03-15 16:41:18,655] [INFO] Query marker FASTA was written to OceanDNA-a1308/markers.fasta
[2023-03-15 16:41:18,656] [INFO] Task started: Blastn
[2023-03-15 16:41:18,656] [INFO] Running command: blastn -query OceanDNA-a1308/markers.fasta -db /var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference/reference_markers.fasta -out OceanDNA-a1308/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:41:22,548] [INFO] Task succeeded: Blastn
[2023-03-15 16:41:22,550] [INFO] Selected 5 target genomes.
[2023-03-15 16:41:22,551] [INFO] Target genome list was writen to OceanDNA-a1308/target_genomes.txt
[2023-03-15 16:41:22,555] [INFO] Task started: fastANI
[2023-03-15 16:41:22,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d3274c5-705a-4cd6-94fe-27e80672fa16/OceanDNA-a1308.fa --refList OceanDNA-a1308/target_genomes.txt --output OceanDNA-a1308/fastani_result.tsv --threads 1
[2023-03-15 16:41:25,168] [INFO] Task succeeded: fastANI
[2023-03-15 16:41:25,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:41:25,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:41:25,169] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:41:25,169] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:41:25,169] [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
--------------------------------------------------------------------------------
[2023-03-15 16:41:25,170] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1308/tc_result.tsv
[2023-03-15 16:41:25,170] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:41:25,170] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:41:25,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference/checkm_data
[2023-03-15 16:41:25,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:41:25,442] [INFO] Task started: CheckM
[2023-03-15 16:41:25,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1308/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1308/checkm_input OceanDNA-a1308/checkm_result
[2023-03-15 16:41:45,151] [INFO] Task succeeded: CheckM
[2023-03-15 16:41:45,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:41:45,161] [INFO] ===== Completeness check finished =====
[2023-03-15 16:41:45,161] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:41:45,161] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1308/markers.fasta)
[2023-03-15 16:41:45,162] [INFO] Task started: Blastn
[2023-03-15 16:41:45,162] [INFO] Running command: blastn -query OceanDNA-a1308/markers.fasta -db /var/lib/cwl/stg01a3ec48-3552-412e-b250-ef31c5ecac6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1308/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:41:45,987] [INFO] Task succeeded: Blastn
[2023-03-15 16:41:45,989] [INFO] Selected 6 target genomes.
[2023-03-15 16:41:45,989] [INFO] Target genome list was writen to OceanDNA-a1308/target_genomes_gtdb.txt
[2023-03-15 16:41:45,996] [INFO] Task started: fastANI
[2023-03-15 16:41:45,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d3274c5-705a-4cd6-94fe-27e80672fa16/OceanDNA-a1308.fa --refList OceanDNA-a1308/target_genomes_gtdb.txt --output OceanDNA-a1308/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:41:48,964] [INFO] Task succeeded: fastANI
[2023-03-15 16:41:48,964] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:41:48,964] [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
--------------------------------------------------------------------------------
[2023-03-15 16:41:48,966] [INFO] GTDB search result was written to OceanDNA-a1308/result_gtdb.tsv
[2023-03-15 16:41:48,967] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:41:48,968] [INFO] DFAST_QC result json was written to OceanDNA-a1308/dqc_result.json
[2023-03-15 16:41:48,969] [INFO] DFAST_QC completed!
[2023-03-15 16:41:48,969] [INFO] Total running time: 0h0m38s