[2023-03-15 06:28:21,434] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,434] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference
[2023-03-15 06:28:22,587] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,587] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,587] [INFO] Running command: cat /var/lib/cwl/stg390d4706-42ac-4918-8d62-ebed35dc6f39/OceanDNA-b41636.fa | prodigal -d OceanDNA-b41636/cds.fna -a OceanDNA-b41636/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:30,431] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:30,431] [INFO] Task started: HMMsearch
[2023-03-15 06:28:30,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b41636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference/reference_markers.hmm OceanDNA-b41636/protein.faa > /dev/null
[2023-03-15 06:28:30,601] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:30,602] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg390d4706-42ac-4918-8d62-ebed35dc6f39/OceanDNA-b41636.fa]
[2023-03-15 06:28:30,613] [INFO] Query marker FASTA was written to OceanDNA-b41636/markers.fasta
[2023-03-15 06:28:30,613] [INFO] Task started: Blastn
[2023-03-15 06:28:30,613] [INFO] Running command: blastn -query OceanDNA-b41636/markers.fasta -db /var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference/reference_markers.fasta -out OceanDNA-b41636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:31,173] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:31,176] [INFO] Selected 35 target genomes.
[2023-03-15 06:28:31,176] [INFO] Target genome list was writen to OceanDNA-b41636/target_genomes.txt
[2023-03-15 06:28:31,194] [INFO] Task started: fastANI
[2023-03-15 06:28:31,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg390d4706-42ac-4918-8d62-ebed35dc6f39/OceanDNA-b41636.fa --refList OceanDNA-b41636/target_genomes.txt --output OceanDNA-b41636/fastani_result.tsv --threads 1
[2023-03-15 06:28:50,695] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:50,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:50,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:50,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:50,696] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:50,696] [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 06:28:50,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41636/tc_result.tsv
[2023-03-15 06:28:50,700] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:50,700] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:50,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference/checkm_data
[2023-03-15 06:28:50,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:50,729] [INFO] Task started: CheckM
[2023-03-15 06:28:50,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41636/checkm_input OceanDNA-b41636/checkm_result
[2023-03-15 06:29:15,578] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:15,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:15,580] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:15,581] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:15,581] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41636/markers.fasta)
[2023-03-15 06:29:15,582] [INFO] Task started: Blastn
[2023-03-15 06:29:15,582] [INFO] Running command: blastn -query OceanDNA-b41636/markers.fasta -db /var/lib/cwl/stgc1c390f2-5748-4526-9ceb-dfea38c400fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:16,454] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:16,459] [INFO] Selected 19 target genomes.
[2023-03-15 06:29:16,459] [INFO] Target genome list was writen to OceanDNA-b41636/target_genomes_gtdb.txt
[2023-03-15 06:29:16,473] [INFO] Task started: fastANI
[2023-03-15 06:29:16,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg390d4706-42ac-4918-8d62-ebed35dc6f39/OceanDNA-b41636.fa --refList OceanDNA-b41636/target_genomes_gtdb.txt --output OceanDNA-b41636/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:25,000] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:25,003] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:29:25,003] [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_002726445.1	s__UBA7434 sp002726445	99.5991	330	469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.17	99.17	0.72	0.72	2	conclusive
GCA_002339085.1	s__UBA7434 sp002339085	88.3603	396	469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	99.78	99.78	0.84	0.84	2	-
GCA_002336035.1	s__UBA7434 sp002336035	79.3153	225	469	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA7434;g__UBA7434	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:25,012] [INFO] GTDB search result was written to OceanDNA-b41636/result_gtdb.tsv
[2023-03-15 06:29:25,012] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:25,012] [INFO] DFAST_QC result json was written to OceanDNA-b41636/dqc_result.json
[2023-03-15 06:29:25,012] [INFO] DFAST_QC completed!
[2023-03-15 06:29:25,013] [INFO] Total running time: 0h1m4s