[2023-03-18 23:11:06,988] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,988] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference
[2023-03-18 23:11:08,184] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,184] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,184] [INFO] Running command: cat /var/lib/cwl/stg4c4c57a1-3fd6-4bf5-9a1e-577ae59e2401/OceanDNA-b16915.fa | prodigal -d OceanDNA-b16915/cds.fna -a OceanDNA-b16915/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:11,170] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:11,170] [INFO] Task started: HMMsearch
[2023-03-18 23:11:11,170] [INFO] Running command: hmmsearch --tblout OceanDNA-b16915/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference/reference_markers.hmm OceanDNA-b16915/protein.faa > /dev/null
[2023-03-18 23:11:11,319] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:11,320] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4c4c57a1-3fd6-4bf5-9a1e-577ae59e2401/OceanDNA-b16915.fa]
[2023-03-18 23:11:11,326] [INFO] Query marker FASTA was written to OceanDNA-b16915/markers.fasta
[2023-03-18 23:11:11,328] [INFO] Task started: Blastn
[2023-03-18 23:11:11,328] [INFO] Running command: blastn -query OceanDNA-b16915/markers.fasta -db /var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference/reference_markers.fasta -out OceanDNA-b16915/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:11,943] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:11,944] [INFO] Selected 12 target genomes.
[2023-03-18 23:11:11,944] [INFO] Target genome list was writen to OceanDNA-b16915/target_genomes.txt
[2023-03-18 23:11:11,949] [INFO] Task started: fastANI
[2023-03-18 23:11:11,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4c57a1-3fd6-4bf5-9a1e-577ae59e2401/OceanDNA-b16915.fa --refList OceanDNA-b16915/target_genomes.txt --output OceanDNA-b16915/fastani_result.tsv --threads 1
[2023-03-18 23:11:16,868] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:16,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:16,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:16,869] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:16,869] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:16,869] [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
--------------------------------------------------------------------------------
[2023-03-18 23:11:16,869] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16915/tc_result.tsv
[2023-03-18 23:11:16,869] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:16,870] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:16,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference/checkm_data
[2023-03-18 23:11:16,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:16,875] [INFO] Task started: CheckM
[2023-03-18 23:11:16,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16915/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16915/checkm_input OceanDNA-b16915/checkm_result
[2023-03-18 23:11:31,350] [INFO] Task succeeded: CheckM
[2023-03-18 23:11:31,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.92%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:11:31,352] [INFO] ===== Completeness check finished =====
[2023-03-18 23:11:31,352] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:11:31,352] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16915/markers.fasta)
[2023-03-18 23:11:31,352] [INFO] Task started: Blastn
[2023-03-18 23:11:31,352] [INFO] Running command: blastn -query OceanDNA-b16915/markers.fasta -db /var/lib/cwl/stg81c28cbf-6c18-4ceb-a20b-f93dff63ae6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16915/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:31,927] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:31,928] [INFO] Selected 14 target genomes.
[2023-03-18 23:11:31,928] [INFO] Target genome list was writen to OceanDNA-b16915/target_genomes_gtdb.txt
[2023-03-18 23:11:31,944] [INFO] Task started: fastANI
[2023-03-18 23:11:31,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c4c57a1-3fd6-4bf5-9a1e-577ae59e2401/OceanDNA-b16915.fa --refList OceanDNA-b16915/target_genomes_gtdb.txt --output OceanDNA-b16915/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:11:35,223] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:35,226] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:11:35,226] [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_002730475.1	s__NP136 sp002730475	89.3595	72	113	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__NP136	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311855.1	s__UBA1144 sp002311855	78.4939	56	113	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__UBA1144	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:11:35,226] [INFO] GTDB search result was written to OceanDNA-b16915/result_gtdb.tsv
[2023-03-18 23:11:35,226] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:11:35,227] [INFO] DFAST_QC result json was written to OceanDNA-b16915/dqc_result.json
[2023-03-18 23:11:35,227] [INFO] DFAST_QC completed!
[2023-03-18 23:11:35,227] [INFO] Total running time: 0h0m28s