[2023-03-19 01:50:01,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference
[2023-03-19 01:50:03,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,564] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,564] [INFO] Running command: cat /var/lib/cwl/stg30d0af06-eefe-4d85-bc64-e2e28745cd08/OceanDNA-b37846.fa | prodigal -d OceanDNA-b37846/cds.fna -a OceanDNA-b37846/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:18,717] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:18,717] [INFO] Task started: HMMsearch
[2023-03-19 01:50:18,717] [INFO] Running command: hmmsearch --tblout OceanDNA-b37846/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference/reference_markers.hmm OceanDNA-b37846/protein.faa > /dev/null
[2023-03-19 01:50:18,905] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:18,906] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg30d0af06-eefe-4d85-bc64-e2e28745cd08/OceanDNA-b37846.fa]
[2023-03-19 01:50:18,924] [INFO] Query marker FASTA was written to OceanDNA-b37846/markers.fasta
[2023-03-19 01:50:18,925] [INFO] Task started: Blastn
[2023-03-19 01:50:18,925] [INFO] Running command: blastn -query OceanDNA-b37846/markers.fasta -db /var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference/reference_markers.fasta -out OceanDNA-b37846/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:19,491] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:19,492] [INFO] Selected 29 target genomes.
[2023-03-19 01:50:19,492] [INFO] Target genome list was writen to OceanDNA-b37846/target_genomes.txt
[2023-03-19 01:50:19,508] [INFO] Task started: fastANI
[2023-03-19 01:50:19,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d0af06-eefe-4d85-bc64-e2e28745cd08/OceanDNA-b37846.fa --refList OceanDNA-b37846/target_genomes.txt --output OceanDNA-b37846/fastani_result.tsv --threads 1
[2023-03-19 01:50:38,843] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:38,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:38,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:38,844] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:38,844] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:38,844] [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
--------------------------------------------------------------------------------
[2023-03-19 01:50:38,844] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37846/tc_result.tsv
[2023-03-19 01:50:38,844] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:38,844] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:38,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference/checkm_data
[2023-03-19 01:50:38,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:38,877] [INFO] Task started: CheckM
[2023-03-19 01:50:38,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37846/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37846/checkm_input OceanDNA-b37846/checkm_result
[2023-03-19 01:51:19,574] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:19,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:19,604] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:19,605] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:19,605] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37846/markers.fasta)
[2023-03-19 01:51:19,606] [INFO] Task started: Blastn
[2023-03-19 01:51:19,606] [INFO] Running command: blastn -query OceanDNA-b37846/markers.fasta -db /var/lib/cwl/stgb20c9ea5-5784-4a66-8058-cdbd212cc12f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37846/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:20,482] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:20,485] [INFO] Selected 14 target genomes.
[2023-03-19 01:51:20,485] [INFO] Target genome list was writen to OceanDNA-b37846/target_genomes_gtdb.txt
[2023-03-19 01:51:20,495] [INFO] Task started: fastANI
[2023-03-19 01:51:20,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d0af06-eefe-4d85-bc64-e2e28745cd08/OceanDNA-b37846.fa --refList OceanDNA-b37846/target_genomes_gtdb.txt --output OceanDNA-b37846/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:27,890] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:27,894] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:51:27,894] [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_016779445.1	s__Luminiphilus sp016779445	98.0282	614	820	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.89	98.12	0.82	0.77	3	conclusive
GCA_002683335.1	s__Luminiphilus sp002683335	93.3141	517	820	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.43	98.43	0.60	0.60	2	-
GCA_002377985.1	s__Luminiphilus sp002377985	78.9867	361	820	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081075.1	s__Luminiphilus sp008081075	77.9013	245	820	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911345.1	s__Luminiphilus sp013911345	77.0762	52	820	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:27,895] [INFO] GTDB search result was written to OceanDNA-b37846/result_gtdb.tsv
[2023-03-19 01:51:27,898] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:27,900] [INFO] DFAST_QC result json was written to OceanDNA-b37846/dqc_result.json
[2023-03-19 01:51:27,900] [INFO] DFAST_QC completed!
[2023-03-19 01:51:27,900] [INFO] Total running time: 0h1m26s