[2023-03-15 23:07:02,633] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,967] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stg090a23a4-780b-4bb6-99b8-b16a394b9395/OceanDNA-b33046.fa | prodigal -d OceanDNA-b33046/cds.fna -a OceanDNA-b33046/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:14,134] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:14,134] [INFO] Task started: HMMsearch
[2023-03-15 23:07:14,134] [INFO] Running command: hmmsearch --tblout OceanDNA-b33046/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference/reference_markers.hmm OceanDNA-b33046/protein.faa > /dev/null
[2023-03-15 23:07:14,311] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:14,311] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg090a23a4-780b-4bb6-99b8-b16a394b9395/OceanDNA-b33046.fa]
[2023-03-15 23:07:14,333] [INFO] Query marker FASTA was written to OceanDNA-b33046/markers.fasta
[2023-03-15 23:07:14,333] [INFO] Task started: Blastn
[2023-03-15 23:07:14,333] [INFO] Running command: blastn -query OceanDNA-b33046/markers.fasta -db /var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference/reference_markers.fasta -out OceanDNA-b33046/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:14,869] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:14,869] [INFO] Selected 18 target genomes.
[2023-03-15 23:07:14,870] [INFO] Target genome list was writen to OceanDNA-b33046/target_genomes.txt
[2023-03-15 23:07:14,918] [INFO] Task started: fastANI
[2023-03-15 23:07:14,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg090a23a4-780b-4bb6-99b8-b16a394b9395/OceanDNA-b33046.fa --refList OceanDNA-b33046/target_genomes.txt --output OceanDNA-b33046/fastani_result.tsv --threads 1
[2023-03-15 23:07:29,451] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:29,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:29,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:29,451] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:29,452] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:07:29,452] [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 23:07:29,452] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33046/tc_result.tsv
[2023-03-15 23:07:29,452] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:29,452] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:29,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference/checkm_data
[2023-03-15 23:07:29,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:29,460] [INFO] Task started: CheckM
[2023-03-15 23:07:29,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33046/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33046/checkm_input OceanDNA-b33046/checkm_result
[2023-03-15 23:07:59,784] [INFO] Task succeeded: CheckM
[2023-03-15 23:07:59,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.62%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:07:59,803] [INFO] ===== Completeness check finished =====
[2023-03-15 23:07:59,803] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:07:59,803] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33046/markers.fasta)
[2023-03-15 23:07:59,804] [INFO] Task started: Blastn
[2023-03-15 23:07:59,804] [INFO] Running command: blastn -query OceanDNA-b33046/markers.fasta -db /var/lib/cwl/stg16266a14-e22d-490d-bba6-3397ebbdbc38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33046/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:00,569] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:00,570] [INFO] Selected 20 target genomes.
[2023-03-15 23:08:00,570] [INFO] Target genome list was writen to OceanDNA-b33046/target_genomes_gtdb.txt
[2023-03-15 23:08:00,607] [INFO] Task started: fastANI
[2023-03-15 23:08:00,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg090a23a4-780b-4bb6-99b8-b16a394b9395/OceanDNA-b33046.fa --refList OceanDNA-b33046/target_genomes_gtdb.txt --output OceanDNA-b33046/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:13,796] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:13,799] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:13,799] [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_018660965.1	s__JABJJH01 sp018660965	84.6602	263	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__JABJJH01	95.0	98.84	98.67	0.82	0.82	3	-
GCA_016764135.1	s__JABJJH01 sp016764135	77.0287	61	316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__JABJJH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:13,804] [INFO] GTDB search result was written to OceanDNA-b33046/result_gtdb.tsv
[2023-03-15 23:08:13,810] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:13,816] [INFO] DFAST_QC result json was written to OceanDNA-b33046/dqc_result.json
[2023-03-15 23:08:13,816] [INFO] DFAST_QC completed!
[2023-03-15 23:08:13,816] [INFO] Total running time: 0h1m11s