[2023-03-16 01:29:15,916] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:29:15,925] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:29:15,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference
[2023-03-16 01:29:18,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:29:18,468] [INFO] Task started: Prodigal
[2023-03-16 01:29:18,468] [INFO] Running command: cat /var/lib/cwl/stg939c6f13-07f9-4c10-871d-6be6c78db40a/OceanDNA-b28257.fa | prodigal -d OceanDNA-b28257/cds.fna -a OceanDNA-b28257/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:29:25,036] [INFO] Task succeeded: Prodigal
[2023-03-16 01:29:25,037] [INFO] Task started: HMMsearch
[2023-03-16 01:29:25,037] [INFO] Running command: hmmsearch --tblout OceanDNA-b28257/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference/reference_markers.hmm OceanDNA-b28257/protein.faa > /dev/null
[2023-03-16 01:29:25,192] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:29:25,193] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg939c6f13-07f9-4c10-871d-6be6c78db40a/OceanDNA-b28257.fa]
[2023-03-16 01:29:25,290] [INFO] Query marker FASTA was written to OceanDNA-b28257/markers.fasta
[2023-03-16 01:29:25,291] [INFO] Task started: Blastn
[2023-03-16 01:29:25,292] [INFO] Running command: blastn -query OceanDNA-b28257/markers.fasta -db /var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference/reference_markers.fasta -out OceanDNA-b28257/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:29:25,808] [INFO] Task succeeded: Blastn
[2023-03-16 01:29:25,838] [INFO] Selected 11 target genomes.
[2023-03-16 01:29:25,839] [INFO] Target genome list was writen to OceanDNA-b28257/target_genomes.txt
[2023-03-16 01:29:25,845] [INFO] Task started: fastANI
[2023-03-16 01:29:25,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg939c6f13-07f9-4c10-871d-6be6c78db40a/OceanDNA-b28257.fa --refList OceanDNA-b28257/target_genomes.txt --output OceanDNA-b28257/fastani_result.tsv --threads 1
[2023-03-16 01:29:30,030] [INFO] Task succeeded: fastANI
[2023-03-16 01:29:30,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:29:30,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:29:30,031] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:29:30,031] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:29:30,031] [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
--------------------------------------------------------------------------------
[2023-03-16 01:29:30,038] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28257/tc_result.tsv
[2023-03-16 01:29:30,050] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:29:30,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:29:30,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference/checkm_data
[2023-03-16 01:29:30,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:29:30,246] [INFO] Task started: CheckM
[2023-03-16 01:29:30,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28257/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28257/checkm_input OceanDNA-b28257/checkm_result
[2023-03-16 01:29:56,460] [INFO] Task succeeded: CheckM
[2023-03-16 01:29:56,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.98%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 01:29:56,633] [INFO] ===== Completeness check finished =====
[2023-03-16 01:29:56,634] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:29:56,634] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28257/markers.fasta)
[2023-03-16 01:29:56,634] [INFO] Task started: Blastn
[2023-03-16 01:29:56,634] [INFO] Running command: blastn -query OceanDNA-b28257/markers.fasta -db /var/lib/cwl/stg9487fa60-9657-4950-aa07-c9f240b9e449/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28257/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:29:57,771] [INFO] Task succeeded: Blastn
[2023-03-16 01:29:57,805] [INFO] Selected 18 target genomes.
[2023-03-16 01:29:57,805] [INFO] Target genome list was writen to OceanDNA-b28257/target_genomes_gtdb.txt
[2023-03-16 01:29:58,373] [INFO] Task started: fastANI
[2023-03-16 01:29:58,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg939c6f13-07f9-4c10-871d-6be6c78db40a/OceanDNA-b28257.fa --refList OceanDNA-b28257/target_genomes_gtdb.txt --output OceanDNA-b28257/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:30:03,429] [INFO] Task succeeded: fastANI
[2023-03-16 01:30:03,432] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 01:30:03,433] [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_902599445.1	s__CACIIZ01 sp902599445	95.2085	217	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902586855.1	s__CACIIZ01 sp902586855	83.7311	118	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699695.2	s__CACIIZ01 sp002699695	81.7918	166	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239455.1	s__CACIIZ01 sp014239455	79.8821	81	368	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:30:03,446] [INFO] GTDB search result was written to OceanDNA-b28257/result_gtdb.tsv
[2023-03-16 01:30:03,467] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:30:03,483] [INFO] DFAST_QC result json was written to OceanDNA-b28257/dqc_result.json
[2023-03-16 01:30:03,483] [INFO] DFAST_QC completed!
[2023-03-16 01:30:03,483] [INFO] Total running time: 0h0m48s