[2023-03-16 07:28:30,029] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference
[2023-03-16 07:28:31,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,146] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,147] [INFO] Running command: cat /var/lib/cwl/stgbd6a7326-09ad-4c34-828f-6707f8760098/OceanDNA-b24678.fa | prodigal -d OceanDNA-b24678/cds.fna -a OceanDNA-b24678/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:41,793] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:41,793] [INFO] Task started: HMMsearch
[2023-03-16 07:28:41,793] [INFO] Running command: hmmsearch --tblout OceanDNA-b24678/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference/reference_markers.hmm OceanDNA-b24678/protein.faa > /dev/null
[2023-03-16 07:28:41,985] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:41,985] [INFO] Found 6/6 markers.
[2023-03-16 07:28:42,001] [INFO] Query marker FASTA was written to OceanDNA-b24678/markers.fasta
[2023-03-16 07:28:42,003] [INFO] Task started: Blastn
[2023-03-16 07:28:42,003] [INFO] Running command: blastn -query OceanDNA-b24678/markers.fasta -db /var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference/reference_markers.fasta -out OceanDNA-b24678/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:42,585] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:42,587] [INFO] Selected 34 target genomes.
[2023-03-16 07:28:42,588] [INFO] Target genome list was writen to OceanDNA-b24678/target_genomes.txt
[2023-03-16 07:28:42,611] [INFO] Task started: fastANI
[2023-03-16 07:28:42,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd6a7326-09ad-4c34-828f-6707f8760098/OceanDNA-b24678.fa --refList OceanDNA-b24678/target_genomes.txt --output OceanDNA-b24678/fastani_result.tsv --threads 1
[2023-03-16 07:29:04,219] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:04,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:29:04,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:29:04,220] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:29:04,220] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:29:04,220] [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 07:29:04,220] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24678/tc_result.tsv
[2023-03-16 07:29:04,220] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:29:04,220] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:29:04,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference/checkm_data
[2023-03-16 07:29:04,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:29:04,234] [INFO] Task started: CheckM
[2023-03-16 07:29:04,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24678/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24678/checkm_input OceanDNA-b24678/checkm_result
[2023-03-16 07:29:35,078] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:35,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:35,082] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:35,082] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:35,083] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24678/markers.fasta)
[2023-03-16 07:29:35,084] [INFO] Task started: Blastn
[2023-03-16 07:29:35,084] [INFO] Running command: blastn -query OceanDNA-b24678/markers.fasta -db /var/lib/cwl/stg5cbe8fad-efec-4be4-aa03-03dd9bf36391/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24678/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:35,998] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:36,000] [INFO] Selected 31 target genomes.
[2023-03-16 07:29:36,000] [INFO] Target genome list was writen to OceanDNA-b24678/target_genomes_gtdb.txt
[2023-03-16 07:29:36,496] [INFO] Task started: fastANI
[2023-03-16 07:29:36,497] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd6a7326-09ad-4c34-828f-6707f8760098/OceanDNA-b24678.fa --refList OceanDNA-b24678/target_genomes_gtdb.txt --output OceanDNA-b24678/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:51,077] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:51,079] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:29:51,079] [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_007117665.1	s__UM-FILTER-47-13 sp007117665	75.6927	50	549	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__Micavibrionaceae;g__UM-FILTER-47-13	95.0	99.52	99.40	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:51,080] [INFO] GTDB search result was written to OceanDNA-b24678/result_gtdb.tsv
[2023-03-16 07:29:51,080] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:51,081] [INFO] DFAST_QC result json was written to OceanDNA-b24678/dqc_result.json
[2023-03-16 07:29:51,081] [INFO] DFAST_QC completed!
[2023-03-16 07:29:51,081] [INFO] Total running time: 0h1m21s