[2023-03-16 08:50:59,692] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,692] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,693] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference
[2023-03-16 08:51:00,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,830] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,830] [INFO] Running command: cat /var/lib/cwl/stg38fa989b-1936-480b-9bdb-9eeed3b364cd/OceanDNA-b15163.fa | prodigal -d OceanDNA-b15163/cds.fna -a OceanDNA-b15163/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:08,419] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:08,419] [INFO] Task started: HMMsearch
[2023-03-16 08:51:08,420] [INFO] Running command: hmmsearch --tblout OceanDNA-b15163/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference/reference_markers.hmm OceanDNA-b15163/protein.faa > /dev/null
[2023-03-16 08:51:08,603] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:08,603] [INFO] Found 6/6 markers.
[2023-03-16 08:51:08,618] [INFO] Query marker FASTA was written to OceanDNA-b15163/markers.fasta
[2023-03-16 08:51:08,619] [INFO] Task started: Blastn
[2023-03-16 08:51:08,620] [INFO] Running command: blastn -query OceanDNA-b15163/markers.fasta -db /var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference/reference_markers.fasta -out OceanDNA-b15163/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:09,141] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:09,143] [INFO] Selected 12 target genomes.
[2023-03-16 08:51:09,143] [INFO] Target genome list was writen to OceanDNA-b15163/target_genomes.txt
[2023-03-16 08:51:09,154] [INFO] Task started: fastANI
[2023-03-16 08:51:09,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg38fa989b-1936-480b-9bdb-9eeed3b364cd/OceanDNA-b15163.fa --refList OceanDNA-b15163/target_genomes.txt --output OceanDNA-b15163/fastani_result.tsv --threads 1
[2023-03-16 08:51:15,749] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:15,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:15,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:15,750] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:15,750] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:51:15,750] [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 08:51:15,751] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15163/tc_result.tsv
[2023-03-16 08:51:15,752] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:15,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:15,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference/checkm_data
[2023-03-16 08:51:15,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:15,759] [INFO] Task started: CheckM
[2023-03-16 08:51:15,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15163/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15163/checkm_input OceanDNA-b15163/checkm_result
[2023-03-16 08:51:40,571] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:40,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:40,579] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:40,579] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:40,579] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15163/markers.fasta)
[2023-03-16 08:51:40,580] [INFO] Task started: Blastn
[2023-03-16 08:51:40,580] [INFO] Running command: blastn -query OceanDNA-b15163/markers.fasta -db /var/lib/cwl/stgdaca3386-6a78-48e7-8872-5f150099bc3e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15163/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:41,295] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:41,297] [INFO] Selected 17 target genomes.
[2023-03-16 08:51:41,297] [INFO] Target genome list was writen to OceanDNA-b15163/target_genomes_gtdb.txt
[2023-03-16 08:51:41,316] [INFO] Task started: fastANI
[2023-03-16 08:51:41,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg38fa989b-1936-480b-9bdb-9eeed3b364cd/OceanDNA-b15163.fa --refList OceanDNA-b15163/target_genomes_gtdb.txt --output OceanDNA-b15163/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:51:51,093] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:51,096] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:51:51,096] [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_009391465.1	s__UBA2963 sp003215215	99.6534	450	467	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2963;f__UBA2963;g__UBA2963	95.0	98.78	97.88	0.86	0.67	6	conclusive
GCA_002719715.1	s__UBA2963 sp002719715	79.9418	111	467	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2963;f__UBA2963;g__UBA2963	95.0	97.87	97.85	0.77	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-16 08:51:51,097] [INFO] GTDB search result was written to OceanDNA-b15163/result_gtdb.tsv
[2023-03-16 08:51:51,098] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:51:51,100] [INFO] DFAST_QC result json was written to OceanDNA-b15163/dqc_result.json
[2023-03-16 08:51:51,100] [INFO] DFAST_QC completed!
[2023-03-16 08:51:51,100] [INFO] Total running time: 0h0m51s