[2023-03-18 23:11:06,969] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference
[2023-03-18 23:11:08,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,282] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,282] [INFO] Running command: cat /var/lib/cwl/stgd5bbbcb8-6734-4630-9c65-8d7cd3ef3b77/OceanDNA-b37851.fa | prodigal -d OceanDNA-b37851/cds.fna -a OceanDNA-b37851/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:17,895] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:17,895] [INFO] Task started: HMMsearch
[2023-03-18 23:11:17,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b37851/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference/reference_markers.hmm OceanDNA-b37851/protein.faa > /dev/null
[2023-03-18 23:11:18,092] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:18,092] [INFO] Found 6/6 markers.
[2023-03-18 23:11:18,107] [INFO] Query marker FASTA was written to OceanDNA-b37851/markers.fasta
[2023-03-18 23:11:18,107] [INFO] Task started: Blastn
[2023-03-18 23:11:18,107] [INFO] Running command: blastn -query OceanDNA-b37851/markers.fasta -db /var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference/reference_markers.fasta -out OceanDNA-b37851/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:18,663] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:18,664] [INFO] Selected 33 target genomes.
[2023-03-18 23:11:18,664] [INFO] Target genome list was writen to OceanDNA-b37851/target_genomes.txt
[2023-03-18 23:11:18,681] [INFO] Task started: fastANI
[2023-03-18 23:11:18,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5bbbcb8-6734-4630-9c65-8d7cd3ef3b77/OceanDNA-b37851.fa --refList OceanDNA-b37851/target_genomes.txt --output OceanDNA-b37851/fastani_result.tsv --threads 1
[2023-03-18 23:11:40,373] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:40,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:40,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:40,373] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:40,373] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:40,373] [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 23:11:40,374] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37851/tc_result.tsv
[2023-03-18 23:11:40,374] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:40,374] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:40,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference/checkm_data
[2023-03-18 23:11:40,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:40,400] [INFO] Task started: CheckM
[2023-03-18 23:11:40,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37851/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37851/checkm_input OceanDNA-b37851/checkm_result
[2023-03-18 23:12:09,433] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:09,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.09%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:09,439] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:09,439] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:09,439] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37851/markers.fasta)
[2023-03-18 23:12:09,439] [INFO] Task started: Blastn
[2023-03-18 23:12:09,439] [INFO] Running command: blastn -query OceanDNA-b37851/markers.fasta -db /var/lib/cwl/stg131ea6ff-40b5-4afc-97ae-ac676068279f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37851/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:10,209] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:10,210] [INFO] Selected 27 target genomes.
[2023-03-18 23:12:10,210] [INFO] Target genome list was writen to OceanDNA-b37851/target_genomes_gtdb.txt
[2023-03-18 23:12:10,237] [INFO] Task started: fastANI
[2023-03-18 23:12:10,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5bbbcb8-6734-4630-9c65-8d7cd3ef3b77/OceanDNA-b37851.fa --refList OceanDNA-b37851/target_genomes_gtdb.txt --output OceanDNA-b37851/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:23,433] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:23,439] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:12:23,439] [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_002377985.1	s__Luminiphilus sp002377985	78.9615	227	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779445.1	s__Luminiphilus sp016779445	78.3985	202	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.89	98.12	0.82	0.77	3	-
GCA_002683335.1	s__Luminiphilus sp002683335	78.2587	167	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.43	98.43	0.60	0.60	2	-
GCA_008081075.1	s__Luminiphilus sp008081075	78.1195	143	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	77.7213	82	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520195.1	s__Luminiphilus sp902520195	77.3652	59	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_002683395.1	s__Luminiphilus sp002683395	77.2591	63	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
GCA_016778045.1	s__Luminiphilus sp016778045	76.8876	71	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721785.1	s__Luminiphilus sp002721785	76.8453	86	497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:23,439] [INFO] GTDB search result was written to OceanDNA-b37851/result_gtdb.tsv
[2023-03-18 23:12:23,439] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:23,440] [INFO] DFAST_QC result json was written to OceanDNA-b37851/dqc_result.json
[2023-03-18 23:12:23,440] [INFO] DFAST_QC completed!
[2023-03-18 23:12:23,440] [INFO] Total running time: 0h1m16s