[2023-03-17 00:02:20,756] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference
[2023-03-17 00:02:21,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,845] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,845] [INFO] Running command: cat /var/lib/cwl/stg2ce64ae8-10be-42a3-9383-0e6f48648878/OceanDNA-b25732.fa | prodigal -d OceanDNA-b25732/cds.fna -a OceanDNA-b25732/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:23,263] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:23,263] [INFO] Task started: HMMsearch
[2023-03-17 00:02:23,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b25732/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference/reference_markers.hmm OceanDNA-b25732/protein.faa > /dev/null
[2023-03-17 00:02:23,401] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:23,402] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2ce64ae8-10be-42a3-9383-0e6f48648878/OceanDNA-b25732.fa]
[2023-03-17 00:02:23,407] [INFO] Query marker FASTA was written to OceanDNA-b25732/markers.fasta
[2023-03-17 00:02:23,409] [INFO] Task started: Blastn
[2023-03-17 00:02:23,409] [INFO] Running command: blastn -query OceanDNA-b25732/markers.fasta -db /var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference/reference_markers.fasta -out OceanDNA-b25732/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:23,965] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:23,966] [INFO] Selected 7 target genomes.
[2023-03-17 00:02:23,966] [INFO] Target genome list was writen to OceanDNA-b25732/target_genomes.txt
[2023-03-17 00:02:24,008] [INFO] Task started: fastANI
[2023-03-17 00:02:24,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce64ae8-10be-42a3-9383-0e6f48648878/OceanDNA-b25732.fa --refList OceanDNA-b25732/target_genomes.txt --output OceanDNA-b25732/fastani_result.tsv --threads 1
[2023-03-17 00:02:26,066] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:26,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:26,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:26,067] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:26,067] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:02:26,067] [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 00:02:26,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25732/tc_result.tsv
[2023-03-17 00:02:26,067] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:26,067] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:26,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference/checkm_data
[2023-03-17 00:02:26,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:26,470] [INFO] Task started: CheckM
[2023-03-17 00:02:26,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25732/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25732/checkm_input OceanDNA-b25732/checkm_result
[2023-03-17 00:02:41,309] [INFO] Task succeeded: CheckM
[2023-03-17 00:02:41,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:02:41,311] [INFO] ===== Completeness check finished =====
[2023-03-17 00:02:41,311] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:02:41,311] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25732/markers.fasta)
[2023-03-17 00:02:41,314] [INFO] Task started: Blastn
[2023-03-17 00:02:41,314] [INFO] Running command: blastn -query OceanDNA-b25732/markers.fasta -db /var/lib/cwl/stg0ddc51f1-48e7-4709-9778-791fcc7e0e2c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25732/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:42,713] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:42,714] [INFO] Selected 15 target genomes.
[2023-03-17 00:02:42,714] [INFO] Target genome list was writen to OceanDNA-b25732/target_genomes_gtdb.txt
[2023-03-17 00:02:42,720] [INFO] Task started: fastANI
[2023-03-17 00:02:42,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce64ae8-10be-42a3-9383-0e6f48648878/OceanDNA-b25732.fa --refList OceanDNA-b25732/target_genomes_gtdb.txt --output OceanDNA-b25732/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:02:44,895] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:44,897] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:02:44,897] [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_902560855.1	s__Pelagibacter sp902560855	81.0348	51	73	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:02:44,898] [INFO] GTDB search result was written to OceanDNA-b25732/result_gtdb.tsv
[2023-03-17 00:02:44,898] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:02:44,898] [INFO] DFAST_QC result json was written to OceanDNA-b25732/dqc_result.json
[2023-03-17 00:02:44,898] [INFO] DFAST_QC completed!
[2023-03-17 00:02:44,898] [INFO] Total running time: 0h0m24s