[2023-03-18 20:13:32,230] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,230] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,230] [INFO] DQC Reference Directory: /var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference
[2023-03-18 20:13:33,436] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,436] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,436] [INFO] Running command: cat /var/lib/cwl/stg9c5d276c-d6a5-4534-9572-4a5a548c0396/OceanDNA-b24781.fa | prodigal -d OceanDNA-b24781/cds.fna -a OceanDNA-b24781/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:48,782] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:48,782] [INFO] Task started: HMMsearch
[2023-03-18 20:13:48,782] [INFO] Running command: hmmsearch --tblout OceanDNA-b24781/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference/reference_markers.hmm OceanDNA-b24781/protein.faa > /dev/null
[2023-03-18 20:13:48,990] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:48,991] [INFO] Found 6/6 markers.
[2023-03-18 20:13:49,013] [INFO] Query marker FASTA was written to OceanDNA-b24781/markers.fasta
[2023-03-18 20:13:49,013] [INFO] Task started: Blastn
[2023-03-18 20:13:49,013] [INFO] Running command: blastn -query OceanDNA-b24781/markers.fasta -db /var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference/reference_markers.fasta -out OceanDNA-b24781/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:49,544] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:49,545] [INFO] Selected 24 target genomes.
[2023-03-18 20:13:49,545] [INFO] Target genome list was writen to OceanDNA-b24781/target_genomes.txt
[2023-03-18 20:13:49,559] [INFO] Task started: fastANI
[2023-03-18 20:13:49,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c5d276c-d6a5-4534-9572-4a5a548c0396/OceanDNA-b24781.fa --refList OceanDNA-b24781/target_genomes.txt --output OceanDNA-b24781/fastani_result.tsv --threads 1
[2023-03-18 20:14:06,290] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:06,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:06,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:06,290] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:06,291] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:14:06,291] [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 20:14:06,291] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24781/tc_result.tsv
[2023-03-18 20:14:06,291] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:06,291] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:06,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference/checkm_data
[2023-03-18 20:14:06,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:06,299] [INFO] Task started: CheckM
[2023-03-18 20:14:06,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24781/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24781/checkm_input OceanDNA-b24781/checkm_result
[2023-03-18 20:14:47,417] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:47,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:47,420] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:47,421] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:47,421] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24781/markers.fasta)
[2023-03-18 20:14:47,421] [INFO] Task started: Blastn
[2023-03-18 20:14:47,421] [INFO] Running command: blastn -query OceanDNA-b24781/markers.fasta -db /var/lib/cwl/stgdafb2373-8440-4c85-8718-3ba7933de1a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24781/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:48,180] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:48,180] [INFO] Selected 22 target genomes.
[2023-03-18 20:14:48,181] [INFO] Target genome list was writen to OceanDNA-b24781/target_genomes_gtdb.txt
[2023-03-18 20:14:48,669] [INFO] Task started: fastANI
[2023-03-18 20:14:48,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c5d276c-d6a5-4534-9572-4a5a548c0396/OceanDNA-b24781.fa --refList OceanDNA-b24781/target_genomes_gtdb.txt --output OceanDNA-b24781/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:04,668] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:04,671] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:15:04,671] [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_002722775.1	s__GCA-2722775 sp002722775	99.4823	457	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__GCA-2722775	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016780745.1	s__JADHLJ01 sp016780745	76.0205	59	846	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:04,671] [INFO] GTDB search result was written to OceanDNA-b24781/result_gtdb.tsv
[2023-03-18 20:15:04,671] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:04,672] [INFO] DFAST_QC result json was written to OceanDNA-b24781/dqc_result.json
[2023-03-18 20:15:04,672] [INFO] DFAST_QC completed!
[2023-03-18 20:15:04,672] [INFO] Total running time: 0h1m32s