[2023-03-17 00:17:04,585] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,585] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,585] [INFO] DQC Reference Directory: /var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference
[2023-03-17 00:17:05,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,675] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,675] [INFO] Running command: cat /var/lib/cwl/stg87b1e9cb-195a-447e-b7b2-df3812fac53a/OceanDNA-b118.fa | prodigal -d OceanDNA-b118/cds.fna -a OceanDNA-b118/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:09,354] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:09,354] [INFO] Task started: HMMsearch
[2023-03-17 00:17:09,354] [INFO] Running command: hmmsearch --tblout OceanDNA-b118/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference/reference_markers.hmm OceanDNA-b118/protein.faa > /dev/null
[2023-03-17 00:17:09,481] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:09,482] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg87b1e9cb-195a-447e-b7b2-df3812fac53a/OceanDNA-b118.fa]
[2023-03-17 00:17:09,493] [INFO] Query marker FASTA was written to OceanDNA-b118/markers.fasta
[2023-03-17 00:17:09,494] [INFO] Task started: Blastn
[2023-03-17 00:17:09,494] [INFO] Running command: blastn -query OceanDNA-b118/markers.fasta -db /var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference/reference_markers.fasta -out OceanDNA-b118/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:09,930] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:09,930] [INFO] Selected 18 target genomes.
[2023-03-17 00:17:09,931] [INFO] Target genome list was writen to OceanDNA-b118/target_genomes.txt
[2023-03-17 00:17:09,941] [INFO] Task started: fastANI
[2023-03-17 00:17:09,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b1e9cb-195a-447e-b7b2-df3812fac53a/OceanDNA-b118.fa --refList OceanDNA-b118/target_genomes.txt --output OceanDNA-b118/fastani_result.tsv --threads 1
[2023-03-17 00:17:20,804] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:20,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:20,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:20,805] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:20,805] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:17:20,805] [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
--------------------------------------------------------------------------------
[2023-03-17 00:17:20,805] [INFO] DFAST Taxonomy check result was written to OceanDNA-b118/tc_result.tsv
[2023-03-17 00:17:20,805] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:20,806] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:20,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference/checkm_data
[2023-03-17 00:17:20,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:20,841] [INFO] Task started: CheckM
[2023-03-17 00:17:20,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b118/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b118/checkm_input OceanDNA-b118/checkm_result
[2023-03-17 00:17:37,137] [INFO] Task succeeded: CheckM
[2023-03-17 00:17:37,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.33%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:17:37,163] [INFO] ===== Completeness check finished =====
[2023-03-17 00:17:37,163] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:17:37,164] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b118/markers.fasta)
[2023-03-17 00:17:37,165] [INFO] Task started: Blastn
[2023-03-17 00:17:37,165] [INFO] Running command: blastn -query OceanDNA-b118/markers.fasta -db /var/lib/cwl/stged032b3f-ff83-4551-9067-3d5e77b4d3c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b118/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:37,628] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:37,629] [INFO] Selected 17 target genomes.
[2023-03-17 00:17:37,629] [INFO] Target genome list was writen to OceanDNA-b118/target_genomes_gtdb.txt
[2023-03-17 00:17:37,677] [INFO] Task started: fastANI
[2023-03-17 00:17:37,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg87b1e9cb-195a-447e-b7b2-df3812fac53a/OceanDNA-b118.fa --refList OceanDNA-b118/target_genomes_gtdb.txt --output OceanDNA-b118/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:17:45,168] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:45,170] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:17:45,170] [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_002346475.1	s__UBA2999 sp002346475	90.4008	111	114	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__UBA2999	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:17:45,171] [INFO] GTDB search result was written to OceanDNA-b118/result_gtdb.tsv
[2023-03-17 00:17:45,171] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:17:45,171] [INFO] DFAST_QC result json was written to OceanDNA-b118/dqc_result.json
[2023-03-17 00:17:45,171] [INFO] DFAST_QC completed!
[2023-03-17 00:17:45,171] [INFO] Total running time: 0h0m41s