[2023-03-15 14:47:21,443] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,444] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference
[2023-03-15 14:47:22,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,571] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,571] [INFO] Running command: cat /var/lib/cwl/stg648e39ca-cadb-4c95-be15-3b89f9484f6f/OceanDNA-b24625.fa | prodigal -d OceanDNA-b24625/cds.fna -a OceanDNA-b24625/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:34,554] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:34,555] [INFO] Task started: HMMsearch
[2023-03-15 14:47:34,555] [INFO] Running command: hmmsearch --tblout OceanDNA-b24625/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference/reference_markers.hmm OceanDNA-b24625/protein.faa > /dev/null
[2023-03-15 14:47:34,743] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:34,743] [INFO] Found 6/6 markers.
[2023-03-15 14:47:34,763] [INFO] Query marker FASTA was written to OceanDNA-b24625/markers.fasta
[2023-03-15 14:47:34,764] [INFO] Task started: Blastn
[2023-03-15 14:47:34,764] [INFO] Running command: blastn -query OceanDNA-b24625/markers.fasta -db /var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference/reference_markers.fasta -out OceanDNA-b24625/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:35,346] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:35,350] [INFO] Selected 24 target genomes.
[2023-03-15 14:47:35,351] [INFO] Target genome list was writen to OceanDNA-b24625/target_genomes.txt
[2023-03-15 14:47:35,362] [INFO] Task started: fastANI
[2023-03-15 14:47:35,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg648e39ca-cadb-4c95-be15-3b89f9484f6f/OceanDNA-b24625.fa --refList OceanDNA-b24625/target_genomes.txt --output OceanDNA-b24625/fastani_result.tsv --threads 1
[2023-03-15 14:47:47,562] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:47,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:47:47,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:47:47,563] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:47:47,563] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:47:47,563] [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 14:47:47,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24625/tc_result.tsv
[2023-03-15 14:47:47,567] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:47:47,567] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:47:47,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference/checkm_data
[2023-03-15 14:47:47,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:47:47,631] [INFO] Task started: CheckM
[2023-03-15 14:47:47,631] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24625/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24625/checkm_input OceanDNA-b24625/checkm_result
[2023-03-15 14:48:21,530] [INFO] Task succeeded: CheckM
[2023-03-15 14:48:21,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 14:48:21,552] [INFO] ===== Completeness check finished =====
[2023-03-15 14:48:21,552] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:48:21,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24625/markers.fasta)
[2023-03-15 14:48:21,552] [INFO] Task started: Blastn
[2023-03-15 14:48:21,552] [INFO] Running command: blastn -query OceanDNA-b24625/markers.fasta -db /var/lib/cwl/stg5375beee-6a5f-4e0a-81c7-9fad109db9e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24625/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:48:22,532] [INFO] Task succeeded: Blastn
[2023-03-15 14:48:22,537] [INFO] Selected 24 target genomes.
[2023-03-15 14:48:22,537] [INFO] Target genome list was writen to OceanDNA-b24625/target_genomes_gtdb.txt
[2023-03-15 14:48:22,698] [INFO] Task started: fastANI
[2023-03-15 14:48:22,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg648e39ca-cadb-4c95-be15-3b89f9484f6f/OceanDNA-b24625.fa --refList OceanDNA-b24625/target_genomes_gtdb.txt --output OceanDNA-b24625/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:48:30,839] [INFO] Task succeeded: fastANI
[2023-03-15 14:48:30,841] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:48:30,841] [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_002167715.1	s__TMED27 sp002167715	99.538	685	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__TMED27	95.0	99.77	99.53	0.97	0.95	3	conclusive
GCA_002687495.1	s__TMED27 sp002687495	77.8558	91	711	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__TMED27	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:48:30,844] [INFO] GTDB search result was written to OceanDNA-b24625/result_gtdb.tsv
[2023-03-15 14:48:30,847] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:48:30,851] [INFO] DFAST_QC result json was written to OceanDNA-b24625/dqc_result.json
[2023-03-15 14:48:30,851] [INFO] DFAST_QC completed!
[2023-03-15 14:48:30,851] [INFO] Total running time: 0h1m9s