[2023-03-15 13:20:51,610] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,610] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,610] [INFO] DQC Reference Directory: /var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference
[2023-03-15 13:20:52,737] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,738] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,738] [INFO] Running command: cat /var/lib/cwl/stg90428d25-258b-4f99-8467-35d2ada8b0a1/OceanDNA-b42522.fa | prodigal -d OceanDNA-b42522/cds.fna -a OceanDNA-b42522/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:20:58,302] [INFO] Task succeeded: Prodigal
[2023-03-15 13:20:58,303] [INFO] Task started: HMMsearch
[2023-03-15 13:20:58,303] [INFO] Running command: hmmsearch --tblout OceanDNA-b42522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference/reference_markers.hmm OceanDNA-b42522/protein.faa > /dev/null
[2023-03-15 13:20:58,553] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:20:58,553] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90428d25-258b-4f99-8467-35d2ada8b0a1/OceanDNA-b42522.fa]
[2023-03-15 13:20:58,565] [INFO] Query marker FASTA was written to OceanDNA-b42522/markers.fasta
[2023-03-15 13:20:58,566] [INFO] Task started: Blastn
[2023-03-15 13:20:58,566] [INFO] Running command: blastn -query OceanDNA-b42522/markers.fasta -db /var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference/reference_markers.fasta -out OceanDNA-b42522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:20:59,169] [INFO] Task succeeded: Blastn
[2023-03-15 13:20:59,170] [INFO] Selected 11 target genomes.
[2023-03-15 13:20:59,171] [INFO] Target genome list was writen to OceanDNA-b42522/target_genomes.txt
[2023-03-15 13:20:59,180] [INFO] Task started: fastANI
[2023-03-15 13:20:59,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg90428d25-258b-4f99-8467-35d2ada8b0a1/OceanDNA-b42522.fa --refList OceanDNA-b42522/target_genomes.txt --output OceanDNA-b42522/fastani_result.tsv --threads 1
[2023-03-15 13:21:04,298] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:04,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:04,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:04,298] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:04,298] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:21:04,298] [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 13:21:04,299] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42522/tc_result.tsv
[2023-03-15 13:21:04,300] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:04,300] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:04,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference/checkm_data
[2023-03-15 13:21:04,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:04,306] [INFO] Task started: CheckM
[2023-03-15 13:21:04,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42522/checkm_input OceanDNA-b42522/checkm_result
[2023-03-15 13:21:25,123] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:25,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.95%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:21:25,125] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:25,125] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:25,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42522/markers.fasta)
[2023-03-15 13:21:25,126] [INFO] Task started: Blastn
[2023-03-15 13:21:25,126] [INFO] Running command: blastn -query OceanDNA-b42522/markers.fasta -db /var/lib/cwl/stgba6a9230-70bf-4a4e-8a36-55e43cfa6185/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:25,916] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:25,918] [INFO] Selected 19 target genomes.
[2023-03-15 13:21:25,918] [INFO] Target genome list was writen to OceanDNA-b42522/target_genomes_gtdb.txt
[2023-03-15 13:21:25,944] [INFO] Task started: fastANI
[2023-03-15 13:21:25,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg90428d25-258b-4f99-8467-35d2ada8b0a1/OceanDNA-b42522.fa --refList OceanDNA-b42522/target_genomes_gtdb.txt --output OceanDNA-b42522/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:21:31,582] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:31,585] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:21:31,585] [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_001628005.1	s__AEGEAN-183 sp001628005	99.5153	321	335	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	99.32	99.31	0.88	0.87	3	conclusive
GCA_012965075.1	s__AEGEAN-183 sp012965075	79.4918	170	335	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	98.73	98.73	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-15 13:21:31,586] [INFO] GTDB search result was written to OceanDNA-b42522/result_gtdb.tsv
[2023-03-15 13:21:31,586] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:21:31,587] [INFO] DFAST_QC result json was written to OceanDNA-b42522/dqc_result.json
[2023-03-15 13:21:31,587] [INFO] DFAST_QC completed!
[2023-03-15 13:21:31,587] [INFO] Total running time: 0h0m40s