[2023-06-17 03:42:07,023] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:42:07,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:42:07,027] [INFO] DQC Reference Directory: /var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference
[2023-06-17 03:42:08,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:42:08,310] [INFO] Task started: Prodigal
[2023-06-17 03:42:08,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg2752b724-c296-4d17-870f-822e56ce04e2/GCA_905620455.1_RIS-SAG-58_genomic.fna.gz | prodigal -d GCA_905620455.1_RIS-SAG-58_genomic.fna/cds.fna -a GCA_905620455.1_RIS-SAG-58_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:42:10,224] [INFO] Task succeeded: Prodigal
[2023-06-17 03:42:10,224] [INFO] Task started: HMMsearch
[2023-06-17 03:42:10,224] [INFO] Running command: hmmsearch --tblout GCA_905620455.1_RIS-SAG-58_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference/reference_markers.hmm GCA_905620455.1_RIS-SAG-58_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:42:10,428] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:42:10,430] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2752b724-c296-4d17-870f-822e56ce04e2/GCA_905620455.1_RIS-SAG-58_genomic.fna.gz]
[2023-06-17 03:42:10,441] [INFO] Query marker FASTA was written to GCA_905620455.1_RIS-SAG-58_genomic.fna/markers.fasta
[2023-06-17 03:42:10,442] [INFO] Task started: Blastn
[2023-06-17 03:42:10,442] [INFO] Running command: blastn -query GCA_905620455.1_RIS-SAG-58_genomic.fna/markers.fasta -db /var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference/reference_markers.fasta -out GCA_905620455.1_RIS-SAG-58_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:42:11,254] [INFO] Task succeeded: Blastn
[2023-06-17 03:42:11,257] [INFO] Selected 13 target genomes.
[2023-06-17 03:42:11,258] [INFO] Target genome list was writen to GCA_905620455.1_RIS-SAG-58_genomic.fna/target_genomes.txt
[2023-06-17 03:42:11,268] [INFO] Task started: fastANI
[2023-06-17 03:42:11,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg2752b724-c296-4d17-870f-822e56ce04e2/GCA_905620455.1_RIS-SAG-58_genomic.fna.gz --refList GCA_905620455.1_RIS-SAG-58_genomic.fna/target_genomes.txt --output GCA_905620455.1_RIS-SAG-58_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:42:17,761] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:17,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:42:17,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:42:17,768] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:42:17,769] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:42:17,769] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	82.9906	167	210	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:42:17,771] [INFO] DFAST Taxonomy check result was written to GCA_905620455.1_RIS-SAG-58_genomic.fna/tc_result.tsv
[2023-06-17 03:42:17,772] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:42:17,772] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:42:17,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference/checkm_data
[2023-06-17 03:42:17,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:42:17,790] [INFO] Task started: CheckM
[2023-06-17 03:42:17,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905620455.1_RIS-SAG-58_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905620455.1_RIS-SAG-58_genomic.fna/checkm_input GCA_905620455.1_RIS-SAG-58_genomic.fna/checkm_result
[2023-06-17 03:42:31,857] [INFO] Task succeeded: CheckM
[2023-06-17 03:42:31,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 15.28%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:42:31,878] [INFO] ===== Completeness check finished =====
[2023-06-17 03:42:31,879] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:42:31,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905620455.1_RIS-SAG-58_genomic.fna/markers.fasta)
[2023-06-17 03:42:31,879] [INFO] Task started: Blastn
[2023-06-17 03:42:31,880] [INFO] Running command: blastn -query GCA_905620455.1_RIS-SAG-58_genomic.fna/markers.fasta -db /var/lib/cwl/stgf92c1233-954a-473e-ab73-1f01e1429c06/dqc_reference/reference_markers_gtdb.fasta -out GCA_905620455.1_RIS-SAG-58_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:42:32,398] [INFO] Task succeeded: Blastn
[2023-06-17 03:42:32,401] [INFO] Selected 12 target genomes.
[2023-06-17 03:42:32,401] [INFO] Target genome list was writen to GCA_905620455.1_RIS-SAG-58_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:42:32,403] [INFO] Task started: fastANI
[2023-06-17 03:42:32,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg2752b724-c296-4d17-870f-822e56ce04e2/GCA_905620455.1_RIS-SAG-58_genomic.fna.gz --refList GCA_905620455.1_RIS-SAG-58_genomic.fna/target_genomes_gtdb.txt --output GCA_905620455.1_RIS-SAG-58_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:42:34,346] [INFO] Task succeeded: fastANI
[2023-06-17 03:42:34,362] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 03:42:34,362] [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_905612465.1	s__Pelagibacter sp905612465	86.8379	102	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616455.1	s__Pelagibacter sp905616455	86.6794	71	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618805.1	s__Pelagibacter sp905618805	86.3535	120	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612495.1	s__Pelagibacter sp905612495	86.3521	105	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618915.1	s__Pelagibacter sp905618915	86.0669	102	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612365.1	s__Pelagibacter sp905612365	85.7093	91	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612525.1	s__Pelagibacter sp905612525	85.001	103	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612335.1	s__Pelagibacter sp905612335	84.9305	89	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905620495.1	s__Pelagibacter sp905620495	84.4485	116	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.77	97.44	0.66	0.65	4	-
GCF_012932795.1	s__Pelagibacter ubique_S	83.6771	169	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618895.1	s__Pelagibacter sp905618895	83.3279	96	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905620465.1	s__Pelagibacter sp905620465	82.4657	67	210	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:42:34,364] [INFO] GTDB search result was written to GCA_905620455.1_RIS-SAG-58_genomic.fna/result_gtdb.tsv
[2023-06-17 03:42:34,365] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:42:34,369] [INFO] DFAST_QC result json was written to GCA_905620455.1_RIS-SAG-58_genomic.fna/dqc_result.json
[2023-06-17 03:42:34,369] [INFO] DFAST_QC completed!
[2023-06-17 03:42:34,369] [INFO] Total running time: 0h0m27s