[2023-03-15 12:33:51,738] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,738] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference
[2023-03-15 12:33:52,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,853] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,853] [INFO] Running command: cat /var/lib/cwl/stg723d4425-1f29-43d2-807b-5facdc2ac739/OceanDNA-b21941.fa | prodigal -d OceanDNA-b21941/cds.fna -a OceanDNA-b21941/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:33:57,682] [INFO] Task succeeded: Prodigal
[2023-03-15 12:33:57,682] [INFO] Task started: HMMsearch
[2023-03-15 12:33:57,682] [INFO] Running command: hmmsearch --tblout OceanDNA-b21941/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference/reference_markers.hmm OceanDNA-b21941/protein.faa > /dev/null
[2023-03-15 12:33:57,828] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:33:57,829] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg723d4425-1f29-43d2-807b-5facdc2ac739/OceanDNA-b21941.fa]
[2023-03-15 12:33:57,835] [INFO] Query marker FASTA was written to OceanDNA-b21941/markers.fasta
[2023-03-15 12:33:57,836] [INFO] Task started: Blastn
[2023-03-15 12:33:57,836] [INFO] Running command: blastn -query OceanDNA-b21941/markers.fasta -db /var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference/reference_markers.fasta -out OceanDNA-b21941/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:33:58,315] [INFO] Task succeeded: Blastn
[2023-03-15 12:33:58,317] [INFO] Selected 16 target genomes.
[2023-03-15 12:33:58,317] [INFO] Target genome list was writen to OceanDNA-b21941/target_genomes.txt
[2023-03-15 12:33:58,327] [INFO] Task started: fastANI
[2023-03-15 12:33:58,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg723d4425-1f29-43d2-807b-5facdc2ac739/OceanDNA-b21941.fa --refList OceanDNA-b21941/target_genomes.txt --output OceanDNA-b21941/fastani_result.tsv --threads 1
[2023-03-15 12:34:09,040] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:09,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:09,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:09,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:09,041] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:34:09,041] [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 12:34:09,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21941/tc_result.tsv
[2023-03-15 12:34:09,042] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:09,042] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:09,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference/checkm_data
[2023-03-15 12:34:09,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:09,048] [INFO] Task started: CheckM
[2023-03-15 12:34:09,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21941/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21941/checkm_input OceanDNA-b21941/checkm_result
[2023-03-15 12:34:27,364] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:27,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:27,366] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:27,366] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:27,366] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21941/markers.fasta)
[2023-03-15 12:34:27,367] [INFO] Task started: Blastn
[2023-03-15 12:34:27,367] [INFO] Running command: blastn -query OceanDNA-b21941/markers.fasta -db /var/lib/cwl/stg70cf0dab-e6e8-4f31-9150-bdd16f8f4911/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21941/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:28,016] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:28,019] [INFO] Selected 19 target genomes.
[2023-03-15 12:34:28,019] [INFO] Target genome list was writen to OceanDNA-b21941/target_genomes_gtdb.txt
[2023-03-15 12:34:28,401] [INFO] Task started: fastANI
[2023-03-15 12:34:28,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg723d4425-1f29-43d2-807b-5facdc2ac739/OceanDNA-b21941.fa --refList OceanDNA-b21941/target_genomes_gtdb.txt --output OceanDNA-b21941/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:34:33,268] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:33,271] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:34:33,271] [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_002376885.1	s__UBA3531 sp002376885	99.9203	202	214	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA3531;g__UBA3531	95.0	99.98	99.98	0.95	0.95	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 12:34:33,271] [INFO] GTDB search result was written to OceanDNA-b21941/result_gtdb.tsv
[2023-03-15 12:34:33,271] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:34:33,272] [INFO] DFAST_QC result json was written to OceanDNA-b21941/dqc_result.json
[2023-03-15 12:34:33,272] [INFO] DFAST_QC completed!
[2023-03-15 12:34:33,272] [INFO] Total running time: 0h0m42s