[2023-03-18 09:41:07,201] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,201] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference
[2023-03-18 09:41:08,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,354] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,354] [INFO] Running command: cat /var/lib/cwl/stg51109068-8d57-4b7d-866e-3f2922749704/OceanDNA-b15137.fa | prodigal -d OceanDNA-b15137/cds.fna -a OceanDNA-b15137/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:27,434] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:27,434] [INFO] Task started: HMMsearch
[2023-03-18 09:41:27,434] [INFO] Running command: hmmsearch --tblout OceanDNA-b15137/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference/reference_markers.hmm OceanDNA-b15137/protein.faa > /dev/null
[2023-03-18 09:41:27,645] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:27,645] [INFO] Found 6/6 markers.
[2023-03-18 09:41:27,667] [INFO] Query marker FASTA was written to OceanDNA-b15137/markers.fasta
[2023-03-18 09:41:27,667] [INFO] Task started: Blastn
[2023-03-18 09:41:27,667] [INFO] Running command: blastn -query OceanDNA-b15137/markers.fasta -db /var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference/reference_markers.fasta -out OceanDNA-b15137/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:28,200] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:28,201] [INFO] Selected 16 target genomes.
[2023-03-18 09:41:28,201] [INFO] Target genome list was writen to OceanDNA-b15137/target_genomes.txt
[2023-03-18 09:41:28,210] [INFO] Task started: fastANI
[2023-03-18 09:41:28,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg51109068-8d57-4b7d-866e-3f2922749704/OceanDNA-b15137.fa --refList OceanDNA-b15137/target_genomes.txt --output OceanDNA-b15137/fastani_result.tsv --threads 1
[2023-03-18 09:41:37,602] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:37,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:37,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:37,603] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:37,603] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:37,603] [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 09:41:37,603] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15137/tc_result.tsv
[2023-03-18 09:41:37,603] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:37,603] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:37,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference/checkm_data
[2023-03-18 09:41:37,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:37,610] [INFO] Task started: CheckM
[2023-03-18 09:41:37,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15137/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15137/checkm_input OceanDNA-b15137/checkm_result
[2023-03-18 09:42:25,590] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:25,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:25,593] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:25,593] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:25,593] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15137/markers.fasta)
[2023-03-18 09:42:25,593] [INFO] Task started: Blastn
[2023-03-18 09:42:25,593] [INFO] Running command: blastn -query OceanDNA-b15137/markers.fasta -db /var/lib/cwl/stg37014ad1-fcee-40e1-be08-1b7796da7d21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15137/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:26,327] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:26,328] [INFO] Selected 23 target genomes.
[2023-03-18 09:42:26,328] [INFO] Target genome list was writen to OceanDNA-b15137/target_genomes_gtdb.txt
[2023-03-18 09:42:26,357] [INFO] Task started: fastANI
[2023-03-18 09:42:26,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg51109068-8d57-4b7d-866e-3f2922749704/OceanDNA-b15137.fa --refList OceanDNA-b15137/target_genomes_gtdb.txt --output OceanDNA-b15137/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:37,655] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:37,658] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:37,658] [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_002238425.1	s__Bin16 sp002238425	76.6644	121	1004	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2963;f__UBA2963;g__Bin16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838965.1	s__Bin16 sp009838965	76.4543	109	1004	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2963;f__UBA2963;g__Bin16	95.0	98.20	97.26	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:37,658] [INFO] GTDB search result was written to OceanDNA-b15137/result_gtdb.tsv
[2023-03-18 09:42:37,658] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:37,658] [INFO] DFAST_QC result json was written to OceanDNA-b15137/dqc_result.json
[2023-03-18 09:42:37,659] [INFO] DFAST_QC completed!
[2023-03-18 09:42:37,659] [INFO] Total running time: 0h1m30s