[2023-03-15 10:49:28,602] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,602] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference
[2023-03-15 10:49:29,803] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,804] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,804] [INFO] Running command: cat /var/lib/cwl/stg798462dc-42ad-4311-95b6-0b39a0af9c5e/OceanDNA-b35857.fa | prodigal -d OceanDNA-b35857/cds.fna -a OceanDNA-b35857/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:40,523] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:40,523] [INFO] Task started: HMMsearch
[2023-03-15 10:49:40,523] [INFO] Running command: hmmsearch --tblout OceanDNA-b35857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference/reference_markers.hmm OceanDNA-b35857/protein.faa > /dev/null
[2023-03-15 10:49:40,730] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:40,730] [INFO] Found 6/6 markers.
[2023-03-15 10:49:40,745] [INFO] Query marker FASTA was written to OceanDNA-b35857/markers.fasta
[2023-03-15 10:49:40,745] [INFO] Task started: Blastn
[2023-03-15 10:49:40,745] [INFO] Running command: blastn -query OceanDNA-b35857/markers.fasta -db /var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference/reference_markers.fasta -out OceanDNA-b35857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:41,330] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:41,331] [INFO] Selected 26 target genomes.
[2023-03-15 10:49:41,331] [INFO] Target genome list was writen to OceanDNA-b35857/target_genomes.txt
[2023-03-15 10:49:41,347] [INFO] Task started: fastANI
[2023-03-15 10:49:41,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg798462dc-42ad-4311-95b6-0b39a0af9c5e/OceanDNA-b35857.fa --refList OceanDNA-b35857/target_genomes.txt --output OceanDNA-b35857/fastani_result.tsv --threads 1
[2023-03-15 10:49:54,416] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:54,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:54,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:54,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:54,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:54,416] [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 10:49:54,417] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35857/tc_result.tsv
[2023-03-15 10:49:54,417] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:54,417] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:54,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference/checkm_data
[2023-03-15 10:49:54,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:54,424] [INFO] Task started: CheckM
[2023-03-15 10:49:54,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35857/checkm_input OceanDNA-b35857/checkm_result
[2023-03-15 10:50:25,407] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:25,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:25,527] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:25,527] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:25,527] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35857/markers.fasta)
[2023-03-15 10:50:25,528] [INFO] Task started: Blastn
[2023-03-15 10:50:25,529] [INFO] Running command: blastn -query OceanDNA-b35857/markers.fasta -db /var/lib/cwl/stg0f76b22d-36c8-4c5a-a896-5fe20f9ecf11/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:26,421] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:26,423] [INFO] Selected 19 target genomes.
[2023-03-15 10:50:26,423] [INFO] Target genome list was writen to OceanDNA-b35857/target_genomes_gtdb.txt
[2023-03-15 10:50:26,450] [INFO] Task started: fastANI
[2023-03-15 10:50:26,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg798462dc-42ad-4311-95b6-0b39a0af9c5e/OceanDNA-b35857.fa --refList OceanDNA-b35857/target_genomes_gtdb.txt --output OceanDNA-b35857/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:36,694] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:36,697] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:50:36,697] [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_002390205.1	s__UBA4457 sp002390205	99.721	501	652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__UBA4457	95.0	99.66	99.66	0.70	0.70	2	conclusive
GCA_018668255.1	s__UBA4457 sp018668255	93.6143	588	652	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__UBA4457	95.0	99.79	99.69	0.94	0.91	8	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:36,698] [INFO] GTDB search result was written to OceanDNA-b35857/result_gtdb.tsv
[2023-03-15 10:50:36,698] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:36,699] [INFO] DFAST_QC result json was written to OceanDNA-b35857/dqc_result.json
[2023-03-15 10:50:36,700] [INFO] DFAST_QC completed!
[2023-03-15 10:50:36,700] [INFO] Total running time: 0h1m8s