[2023-03-18 08:55:50,544] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,544] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference
[2023-03-18 08:55:51,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,757] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,757] [INFO] Running command: cat /var/lib/cwl/stg62a9a834-778f-41cb-be66-013edff9d7ac/OceanDNA-b31325.fa | prodigal -d OceanDNA-b31325/cds.fna -a OceanDNA-b31325/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:54,161] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:54,161] [INFO] Task started: HMMsearch
[2023-03-18 08:55:54,161] [INFO] Running command: hmmsearch --tblout OceanDNA-b31325/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference/reference_markers.hmm OceanDNA-b31325/protein.faa > /dev/null
[2023-03-18 08:55:54,309] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:54,310] [INFO] Found 6/6 markers.
[2023-03-18 08:55:54,316] [INFO] Query marker FASTA was written to OceanDNA-b31325/markers.fasta
[2023-03-18 08:55:54,317] [INFO] Task started: Blastn
[2023-03-18 08:55:54,317] [INFO] Running command: blastn -query OceanDNA-b31325/markers.fasta -db /var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference/reference_markers.fasta -out OceanDNA-b31325/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:55:54,882] [INFO] Task succeeded: Blastn
[2023-03-18 08:55:54,882] [INFO] Selected 8 target genomes.
[2023-03-18 08:55:54,883] [INFO] Target genome list was writen to OceanDNA-b31325/target_genomes.txt
[2023-03-18 08:55:54,889] [INFO] Task started: fastANI
[2023-03-18 08:55:54,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg62a9a834-778f-41cb-be66-013edff9d7ac/OceanDNA-b31325.fa --refList OceanDNA-b31325/target_genomes.txt --output OceanDNA-b31325/fastani_result.tsv --threads 1
[2023-03-18 08:55:57,544] [INFO] Task succeeded: fastANI
[2023-03-18 08:55:57,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:55:57,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:55:57,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:55:57,545] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:55:57,545] [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 08:55:57,551] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31325/tc_result.tsv
[2023-03-18 08:55:57,552] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:55:57,552] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:55:57,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference/checkm_data
[2023-03-18 08:55:57,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:55:57,557] [INFO] Task started: CheckM
[2023-03-18 08:55:57,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31325/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31325/checkm_input OceanDNA-b31325/checkm_result
[2023-03-18 08:56:11,705] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:11,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:11,707] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:11,707] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:11,708] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31325/markers.fasta)
[2023-03-18 08:56:11,709] [INFO] Task started: Blastn
[2023-03-18 08:56:11,709] [INFO] Running command: blastn -query OceanDNA-b31325/markers.fasta -db /var/lib/cwl/stg589841e1-bd99-4d05-a7ec-74ab7efa470a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31325/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:12,658] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:12,659] [INFO] Selected 7 target genomes.
[2023-03-18 08:56:12,659] [INFO] Target genome list was writen to OceanDNA-b31325/target_genomes_gtdb.txt
[2023-03-18 08:56:12,674] [INFO] Task started: fastANI
[2023-03-18 08:56:12,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg62a9a834-778f-41cb-be66-013edff9d7ac/OceanDNA-b31325.fa --refList OceanDNA-b31325/target_genomes_gtdb.txt --output OceanDNA-b31325/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:14,775] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:14,780] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 08:56:14,781] [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_001648025.1	s__Wolbachia sp001648025	96.2731	108	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_014107455.1	s__Wolbachia pipientis_B	96.1749	116	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.0	96.48	96.27	0.84	0.82	4	inconclusive
GCF_000008025.1	s__Wolbachia pipientis	94.3699	122	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.0	99.17	95.93	0.97	0.84	996	-
GCA_902636535.1	s__Wolbachia sp902636535	93.8877	118	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.0	99.78	99.73	0.98	0.96	22	-
GCF_018141665.1	s__Wolbachia sp001439985	86.4904	117	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.5661	96.57	95.97	0.90	0.74	19	-
GCF_013096535.2	s__Wolbachia sp013096535	86.2972	118	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.4261	99.11	95.56	0.97	0.83	21	-
GCF_014771645.1	s__Wolbachia massiliensis	84.265	112	126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Anaplasmataceae;g__Wolbachia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:14,781] [INFO] GTDB search result was written to OceanDNA-b31325/result_gtdb.tsv
[2023-03-18 08:56:14,781] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:14,782] [INFO] DFAST_QC result json was written to OceanDNA-b31325/dqc_result.json
[2023-03-18 08:56:14,782] [INFO] DFAST_QC completed!
[2023-03-18 08:56:14,782] [INFO] Total running time: 0h0m24s