[2023-03-16 21:13:50,883] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:13:50,883] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:13:50,883] [INFO] DQC Reference Directory: /var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference
[2023-03-16 21:13:52,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:13:52,581] [INFO] Task started: Prodigal
[2023-03-16 21:13:52,581] [INFO] Running command: cat /var/lib/cwl/stgf4a1841c-4146-4bfd-8144-dcb19109dc64/OceanDNA-b26949.fa | prodigal -d OceanDNA-b26949/cds.fna -a OceanDNA-b26949/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:13:57,976] [INFO] Task succeeded: Prodigal
[2023-03-16 21:13:57,976] [INFO] Task started: HMMsearch
[2023-03-16 21:13:57,976] [INFO] Running command: hmmsearch --tblout OceanDNA-b26949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference/reference_markers.hmm OceanDNA-b26949/protein.faa > /dev/null
[2023-03-16 21:13:58,161] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:13:58,161] [INFO] Found 6/6 markers.
[2023-03-16 21:13:58,170] [INFO] Query marker FASTA was written to OceanDNA-b26949/markers.fasta
[2023-03-16 21:13:58,172] [INFO] Task started: Blastn
[2023-03-16 21:13:58,172] [INFO] Running command: blastn -query OceanDNA-b26949/markers.fasta -db /var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference/reference_markers.fasta -out OceanDNA-b26949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:13:58,969] [INFO] Task succeeded: Blastn
[2023-03-16 21:13:58,969] [INFO] Selected 26 target genomes.
[2023-03-16 21:13:58,970] [INFO] Target genome list was writen to OceanDNA-b26949/target_genomes.txt
[2023-03-16 21:13:58,988] [INFO] Task started: fastANI
[2023-03-16 21:13:58,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4a1841c-4146-4bfd-8144-dcb19109dc64/OceanDNA-b26949.fa --refList OceanDNA-b26949/target_genomes.txt --output OceanDNA-b26949/fastani_result.tsv --threads 1
[2023-03-16 21:14:12,211] [INFO] Task succeeded: fastANI
[2023-03-16 21:14:12,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:14:12,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:14:12,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:14:12,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:14:12,212] [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 21:14:12,212] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26949/tc_result.tsv
[2023-03-16 21:14:12,212] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:14:12,213] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:14:12,213] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference/checkm_data
[2023-03-16 21:14:12,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:14:12,217] [INFO] Task started: CheckM
[2023-03-16 21:14:12,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26949/checkm_input OceanDNA-b26949/checkm_result
[2023-03-16 21:14:28,950] [INFO] Task succeeded: CheckM
[2023-03-16 21:14:28,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:14:28,952] [INFO] ===== Completeness check finished =====
[2023-03-16 21:14:28,952] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:14:28,952] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26949/markers.fasta)
[2023-03-16 21:14:28,953] [INFO] Task started: Blastn
[2023-03-16 21:14:28,953] [INFO] Running command: blastn -query OceanDNA-b26949/markers.fasta -db /var/lib/cwl/stg95c04a31-d97e-442a-b41a-ae500320c96d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:14:29,799] [INFO] Task succeeded: Blastn
[2023-03-16 21:14:29,800] [INFO] Selected 7 target genomes.
[2023-03-16 21:14:29,800] [INFO] Target genome list was writen to OceanDNA-b26949/target_genomes_gtdb.txt
[2023-03-16 21:14:29,831] [INFO] Task started: fastANI
[2023-03-16 21:14:29,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4a1841c-4146-4bfd-8144-dcb19109dc64/OceanDNA-b26949.fa --refList OceanDNA-b26949/target_genomes_gtdb.txt --output OceanDNA-b26949/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:14:31,370] [INFO] Task succeeded: fastANI
[2023-03-16 21:14:31,375] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:14:31,375] [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_902608415.1	s__AG-430-B22 sp902608415	95.1212	194	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002726005.1	s__AG-430-B22 sp002726005	92.9442	225	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.76	98.76	0.74	0.74	2	-
GCA_003212795.1	s__AG-430-B22 sp003212795	92.6685	267	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	98.52	95.66	0.95	0.87	7	-
GCA_902609025.1	s__AG-430-B22 sp902609025	92.0973	174	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533755.1	s__AG-430-B22 sp902533755	92.0689	180	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	99.48	99.48	0.87	0.87	3	-
GCA_003209955.1	s__AG-430-B22 sp003209955	91.6208	227	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002728335.1	s__AG-430-B22 sp002728335	83.6822	204	281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__AG-430-B22	95.0	97.53	96.38	0.78	0.71	4	-
--------------------------------------------------------------------------------
[2023-03-16 21:14:31,375] [INFO] GTDB search result was written to OceanDNA-b26949/result_gtdb.tsv
[2023-03-16 21:14:31,375] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:14:31,376] [INFO] DFAST_QC result json was written to OceanDNA-b26949/dqc_result.json
[2023-03-16 21:14:31,376] [INFO] DFAST_QC completed!
[2023-03-16 21:14:31,376] [INFO] Total running time: 0h0m40s