[2023-03-15 18:39:12,263] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,263] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,263] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference
[2023-03-15 18:39:13,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,657] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,658] [INFO] Running command: cat /var/lib/cwl/stg744eff21-0612-460d-b2d6-7eafe83ae53f/OceanDNA-b5418.fa | prodigal -d OceanDNA-b5418/cds.fna -a OceanDNA-b5418/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:22,100] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:22,101] [INFO] Task started: HMMsearch
[2023-03-15 18:39:22,101] [INFO] Running command: hmmsearch --tblout OceanDNA-b5418/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference/reference_markers.hmm OceanDNA-b5418/protein.faa > /dev/null
[2023-03-15 18:39:22,258] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:22,258] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg744eff21-0612-460d-b2d6-7eafe83ae53f/OceanDNA-b5418.fa]
[2023-03-15 18:39:22,272] [INFO] Query marker FASTA was written to OceanDNA-b5418/markers.fasta
[2023-03-15 18:39:22,272] [INFO] Task started: Blastn
[2023-03-15 18:39:22,273] [INFO] Running command: blastn -query OceanDNA-b5418/markers.fasta -db /var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference/reference_markers.fasta -out OceanDNA-b5418/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:22,827] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:22,827] [INFO] Selected 27 target genomes.
[2023-03-15 18:39:22,828] [INFO] Target genome list was writen to OceanDNA-b5418/target_genomes.txt
[2023-03-15 18:39:22,841] [INFO] Task started: fastANI
[2023-03-15 18:39:22,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg744eff21-0612-460d-b2d6-7eafe83ae53f/OceanDNA-b5418.fa --refList OceanDNA-b5418/target_genomes.txt --output OceanDNA-b5418/fastani_result.tsv --threads 1
[2023-03-15 18:39:37,245] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:37,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:37,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:37,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:39:37,247] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 18:39:37,247] [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 18:39:37,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5418/tc_result.tsv
[2023-03-15 18:39:37,247] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:37,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:37,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference/checkm_data
[2023-03-15 18:39:37,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:37,255] [INFO] Task started: CheckM
[2023-03-15 18:39:37,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5418/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5418/checkm_input OceanDNA-b5418/checkm_result
[2023-03-15 18:40:03,974] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:03,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:03,977] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:03,977] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:03,977] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5418/markers.fasta)
[2023-03-15 18:40:03,978] [INFO] Task started: Blastn
[2023-03-15 18:40:03,978] [INFO] Running command: blastn -query OceanDNA-b5418/markers.fasta -db /var/lib/cwl/stg2ca7a4e0-38e1-47b9-96fd-face0aba2b2a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5418/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:04,850] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:04,851] [INFO] Selected 30 target genomes.
[2023-03-15 18:40:04,851] [INFO] Target genome list was writen to OceanDNA-b5418/target_genomes_gtdb.txt
[2023-03-15 18:40:05,593] [INFO] Task started: fastANI
[2023-03-15 18:40:05,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg744eff21-0612-460d-b2d6-7eafe83ae53f/OceanDNA-b5418.fa --refList OceanDNA-b5418/target_genomes_gtdb.txt --output OceanDNA-b5418/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:17,737] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:17,740] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:40:17,740] [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_002696025.1	s__UBA952 sp002696025	87.0486	199	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:17,740] [INFO] GTDB search result was written to OceanDNA-b5418/result_gtdb.tsv
[2023-03-15 18:40:17,740] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:17,740] [INFO] DFAST_QC result json was written to OceanDNA-b5418/dqc_result.json
[2023-03-15 18:40:17,741] [INFO] DFAST_QC completed!
[2023-03-15 18:40:17,741] [INFO] Total running time: 0h1m5s