[2023-03-19 05:01:20,078] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:01:20,078] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:01:20,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference
[2023-03-19 05:01:21,177] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:01:21,178] [INFO] Task started: Prodigal
[2023-03-19 05:01:21,178] [INFO] Running command: cat /var/lib/cwl/stg78b91b6b-61b7-42ed-8eff-d5ffe028afa8/OceanDNA-b40235.fa | prodigal -d OceanDNA-b40235/cds.fna -a OceanDNA-b40235/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:01:30,485] [INFO] Task succeeded: Prodigal
[2023-03-19 05:01:30,486] [INFO] Task started: HMMsearch
[2023-03-19 05:01:30,486] [INFO] Running command: hmmsearch --tblout OceanDNA-b40235/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference/reference_markers.hmm OceanDNA-b40235/protein.faa > /dev/null
[2023-03-19 05:01:30,665] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:01:30,665] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg78b91b6b-61b7-42ed-8eff-d5ffe028afa8/OceanDNA-b40235.fa]
[2023-03-19 05:01:30,681] [INFO] Query marker FASTA was written to OceanDNA-b40235/markers.fasta
[2023-03-19 05:01:30,682] [INFO] Task started: Blastn
[2023-03-19 05:01:30,682] [INFO] Running command: blastn -query OceanDNA-b40235/markers.fasta -db /var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference/reference_markers.fasta -out OceanDNA-b40235/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:01:31,200] [INFO] Task succeeded: Blastn
[2023-03-19 05:01:31,201] [INFO] Selected 25 target genomes.
[2023-03-19 05:01:31,201] [INFO] Target genome list was writen to OceanDNA-b40235/target_genomes.txt
[2023-03-19 05:01:31,218] [INFO] Task started: fastANI
[2023-03-19 05:01:31,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg78b91b6b-61b7-42ed-8eff-d5ffe028afa8/OceanDNA-b40235.fa --refList OceanDNA-b40235/target_genomes.txt --output OceanDNA-b40235/fastani_result.tsv --threads 1
[2023-03-19 05:01:45,579] [INFO] Task succeeded: fastANI
[2023-03-19 05:01:45,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:01:45,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:01:45,579] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:01:45,579] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:01:45,579] [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
--------------------------------------------------------------------------------
[2023-03-19 05:01:45,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40235/tc_result.tsv
[2023-03-19 05:01:45,580] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:01:45,580] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:01:45,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference/checkm_data
[2023-03-19 05:01:45,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:01:45,620] [INFO] Task started: CheckM
[2023-03-19 05:01:45,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40235/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40235/checkm_input OceanDNA-b40235/checkm_result
[2023-03-19 05:02:14,544] [INFO] Task succeeded: CheckM
[2023-03-19 05:02:14,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.29%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-03-19 05:02:14,547] [INFO] ===== Completeness check finished =====
[2023-03-19 05:02:14,547] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:02:14,547] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40235/markers.fasta)
[2023-03-19 05:02:14,547] [INFO] Task started: Blastn
[2023-03-19 05:02:14,547] [INFO] Running command: blastn -query OceanDNA-b40235/markers.fasta -db /var/lib/cwl/stg49c47d7a-608c-41bf-9c3f-19e46411ee77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40235/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:02:15,235] [INFO] Task succeeded: Blastn
[2023-03-19 05:02:15,236] [INFO] Selected 21 target genomes.
[2023-03-19 05:02:15,236] [INFO] Target genome list was writen to OceanDNA-b40235/target_genomes_gtdb.txt
[2023-03-19 05:02:15,257] [INFO] Task started: fastANI
[2023-03-19 05:02:15,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg78b91b6b-61b7-42ed-8eff-d5ffe028afa8/OceanDNA-b40235.fa --refList OceanDNA-b40235/target_genomes_gtdb.txt --output OceanDNA-b40235/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:02:27,655] [INFO] Task succeeded: fastANI
[2023-03-19 05:02:27,657] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:02:27,657] [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_018698975.1	s__RFVC01 sp018698975	96.4062	461	499	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__RFVC01	95.0	99.67	99.67	0.94	0.94	2	conclusive
--------------------------------------------------------------------------------
[2023-03-19 05:02:27,657] [INFO] GTDB search result was written to OceanDNA-b40235/result_gtdb.tsv
[2023-03-19 05:02:27,657] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:02:27,657] [INFO] DFAST_QC result json was written to OceanDNA-b40235/dqc_result.json
[2023-03-19 05:02:27,658] [INFO] DFAST_QC completed!
[2023-03-19 05:02:27,658] [INFO] Total running time: 0h1m8s