[2023-03-15 07:25:31,263] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,264] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,264] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference
[2023-03-15 07:25:32,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,917] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,917] [INFO] Running command: cat /var/lib/cwl/stg6ea634e6-1f1a-46a4-98a7-ec10c292f3e3/OceanDNA-b33792.fa | prodigal -d OceanDNA-b33792/cds.fna -a OceanDNA-b33792/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:35,082] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:35,082] [INFO] Task started: HMMsearch
[2023-03-15 07:25:35,082] [INFO] Running command: hmmsearch --tblout OceanDNA-b33792/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference/reference_markers.hmm OceanDNA-b33792/protein.faa > /dev/null
[2023-03-15 07:25:35,333] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:35,334] [INFO] Found 6/6 markers.
[2023-03-15 07:25:35,346] [INFO] Query marker FASTA was written to OceanDNA-b33792/markers.fasta
[2023-03-15 07:25:35,347] [INFO] Task started: Blastn
[2023-03-15 07:25:35,347] [INFO] Running command: blastn -query OceanDNA-b33792/markers.fasta -db /var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference/reference_markers.fasta -out OceanDNA-b33792/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:37,751] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:37,757] [INFO] Selected 18 target genomes.
[2023-03-15 07:25:37,757] [INFO] Target genome list was writen to OceanDNA-b33792/target_genomes.txt
[2023-03-15 07:25:37,768] [INFO] Task started: fastANI
[2023-03-15 07:25:37,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ea634e6-1f1a-46a4-98a7-ec10c292f3e3/OceanDNA-b33792.fa --refList OceanDNA-b33792/target_genomes.txt --output OceanDNA-b33792/fastani_result.tsv --threads 1
[2023-03-15 07:25:46,643] [INFO] Task succeeded: fastANI
[2023-03-15 07:25:46,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:25:46,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:25:46,644] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:25:46,644] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:25:46,644] [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 07:25:46,647] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33792/tc_result.tsv
[2023-03-15 07:25:46,651] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:25:46,652] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:25:46,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference/checkm_data
[2023-03-15 07:25:46,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:25:46,675] [INFO] Task started: CheckM
[2023-03-15 07:25:46,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33792/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33792/checkm_input OceanDNA-b33792/checkm_result
[2023-03-15 07:25:59,689] [INFO] Task succeeded: CheckM
[2023-03-15 07:25:59,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:25:59,755] [INFO] ===== Completeness check finished =====
[2023-03-15 07:25:59,755] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:25:59,755] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33792/markers.fasta)
[2023-03-15 07:25:59,755] [INFO] Task started: Blastn
[2023-03-15 07:25:59,755] [INFO] Running command: blastn -query OceanDNA-b33792/markers.fasta -db /var/lib/cwl/stg0ccd8cb0-35c2-4012-8bec-930afa8cb245/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33792/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:26:00,883] [INFO] Task succeeded: Blastn
[2023-03-15 07:26:00,886] [INFO] Selected 19 target genomes.
[2023-03-15 07:26:00,886] [INFO] Target genome list was writen to OceanDNA-b33792/target_genomes_gtdb.txt
[2023-03-15 07:26:00,931] [INFO] Task started: fastANI
[2023-03-15 07:26:00,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ea634e6-1f1a-46a4-98a7-ec10c292f3e3/OceanDNA-b33792.fa --refList OceanDNA-b33792/target_genomes_gtdb.txt --output OceanDNA-b33792/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:26:05,819] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:05,822] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:26:05,822] [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_905181685.1	s__BACL14 sp905181685	93.6646	67	102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657165.1	s__BACL14 sp018657165	80.6464	60	102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.24	99.09	0.82	0.76	15	-
GCA_018607785.1	s__BACL14 sp018607785	80.0147	72	102	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.17	98.94	0.86	0.81	5	-
--------------------------------------------------------------------------------
[2023-03-15 07:26:05,833] [INFO] GTDB search result was written to OceanDNA-b33792/result_gtdb.tsv
[2023-03-15 07:26:05,847] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:26:05,857] [INFO] DFAST_QC result json was written to OceanDNA-b33792/dqc_result.json
[2023-03-15 07:26:05,858] [INFO] DFAST_QC completed!
[2023-03-15 07:26:05,858] [INFO] Total running time: 0h0m35s