[2023-03-16 01:29:15,913] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:29:15,919] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:29:15,919] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference
[2023-03-16 01:29:18,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:29:18,468] [INFO] Task started: Prodigal
[2023-03-16 01:29:18,468] [INFO] Running command: cat /var/lib/cwl/stg120a96d5-7b82-43d2-a3ae-eb12676ea125/OceanDNA-b12513.fa | prodigal -d OceanDNA-b12513/cds.fna -a OceanDNA-b12513/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:29:21,772] [INFO] Task succeeded: Prodigal
[2023-03-16 01:29:21,772] [INFO] Task started: HMMsearch
[2023-03-16 01:29:21,772] [INFO] Running command: hmmsearch --tblout OceanDNA-b12513/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference/reference_markers.hmm OceanDNA-b12513/protein.faa > /dev/null
[2023-03-16 01:29:21,927] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:29:21,927] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg120a96d5-7b82-43d2-a3ae-eb12676ea125/OceanDNA-b12513.fa]
[2023-03-16 01:29:21,972] [INFO] Query marker FASTA was written to OceanDNA-b12513/markers.fasta
[2023-03-16 01:29:21,975] [INFO] Task started: Blastn
[2023-03-16 01:29:21,975] [INFO] Running command: blastn -query OceanDNA-b12513/markers.fasta -db /var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference/reference_markers.fasta -out OceanDNA-b12513/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:29:25,620] [INFO] Task succeeded: Blastn
[2023-03-16 01:29:25,626] [INFO] Selected 15 target genomes.
[2023-03-16 01:29:25,626] [INFO] Target genome list was writen to OceanDNA-b12513/target_genomes.txt
[2023-03-16 01:29:25,665] [INFO] Task started: fastANI
[2023-03-16 01:29:25,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg120a96d5-7b82-43d2-a3ae-eb12676ea125/OceanDNA-b12513.fa --refList OceanDNA-b12513/target_genomes.txt --output OceanDNA-b12513/fastani_result.tsv --threads 1
[2023-03-16 01:29:33,262] [INFO] Task succeeded: fastANI
[2023-03-16 01:29:33,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:29:33,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:29:33,263] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:29:33,263] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:29:33,263] [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
--------------------------------------------------------------------------------
[2023-03-16 01:29:33,266] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12513/tc_result.tsv
[2023-03-16 01:29:33,269] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:29:33,270] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:29:33,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference/checkm_data
[2023-03-16 01:29:33,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:29:33,282] [INFO] Task started: CheckM
[2023-03-16 01:29:33,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12513/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12513/checkm_input OceanDNA-b12513/checkm_result
[2023-03-16 01:29:55,936] [INFO] Task succeeded: CheckM
[2023-03-16 01:29:55,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:29:56,119] [INFO] ===== Completeness check finished =====
[2023-03-16 01:29:56,120] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:29:56,120] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12513/markers.fasta)
[2023-03-16 01:29:56,122] [INFO] Task started: Blastn
[2023-03-16 01:29:56,122] [INFO] Running command: blastn -query OceanDNA-b12513/markers.fasta -db /var/lib/cwl/stgeaf24676-2647-4745-8103-fd86151f977b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12513/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:29:57,461] [INFO] Task succeeded: Blastn
[2023-03-16 01:29:57,492] [INFO] Selected 18 target genomes.
[2023-03-16 01:29:57,492] [INFO] Target genome list was writen to OceanDNA-b12513/target_genomes_gtdb.txt
[2023-03-16 01:29:58,155] [INFO] Task started: fastANI
[2023-03-16 01:29:58,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg120a96d5-7b82-43d2-a3ae-eb12676ea125/OceanDNA-b12513.fa --refList OceanDNA-b12513/target_genomes_gtdb.txt --output OceanDNA-b12513/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:30:05,704] [INFO] Task succeeded: fastANI
[2023-03-16 01:30:05,705] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:30:05,705] [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
--------------------------------------------------------------------------------
[2023-03-16 01:30:05,717] [INFO] GTDB search result was written to OceanDNA-b12513/result_gtdb.tsv
[2023-03-16 01:30:05,738] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:30:05,748] [INFO] DFAST_QC result json was written to OceanDNA-b12513/dqc_result.json
[2023-03-16 01:30:05,748] [INFO] DFAST_QC completed!
[2023-03-16 01:30:05,748] [INFO] Total running time: 0h0m50s