[2023-06-17 01:33:16,507] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:33:16,509] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:33:16,510] [INFO] DQC Reference Directory: /var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference
[2023-06-17 01:33:17,727] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:33:17,728] [INFO] Task started: Prodigal
[2023-06-17 01:33:17,728] [INFO] Running command: gunzip -c /var/lib/cwl/stgceb048a7-94a8-405e-8ecb-b068e17aa28b/GCA_905620425.1_RIS-SAG-66_genomic.fna.gz | prodigal -d GCA_905620425.1_RIS-SAG-66_genomic.fna/cds.fna -a GCA_905620425.1_RIS-SAG-66_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:33:19,914] [INFO] Task succeeded: Prodigal
[2023-06-17 01:33:19,915] [INFO] Task started: HMMsearch
[2023-06-17 01:33:19,915] [INFO] Running command: hmmsearch --tblout GCA_905620425.1_RIS-SAG-66_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference/reference_markers.hmm GCA_905620425.1_RIS-SAG-66_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:33:20,096] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:33:20,097] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgceb048a7-94a8-405e-8ecb-b068e17aa28b/GCA_905620425.1_RIS-SAG-66_genomic.fna.gz]
[2023-06-17 01:33:20,115] [INFO] Query marker FASTA was written to GCA_905620425.1_RIS-SAG-66_genomic.fna/markers.fasta
[2023-06-17 01:33:20,115] [INFO] Task started: Blastn
[2023-06-17 01:33:20,115] [INFO] Running command: blastn -query GCA_905620425.1_RIS-SAG-66_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference/reference_markers.fasta -out GCA_905620425.1_RIS-SAG-66_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:33:20,876] [INFO] Task succeeded: Blastn
[2023-06-17 01:33:20,881] [INFO] Selected 17 target genomes.
[2023-06-17 01:33:20,881] [INFO] Target genome list was writen to GCA_905620425.1_RIS-SAG-66_genomic.fna/target_genomes.txt
[2023-06-17 01:33:20,891] [INFO] Task started: fastANI
[2023-06-17 01:33:20,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb048a7-94a8-405e-8ecb-b068e17aa28b/GCA_905620425.1_RIS-SAG-66_genomic.fna.gz --refList GCA_905620425.1_RIS-SAG-66_genomic.fna/target_genomes.txt --output GCA_905620425.1_RIS-SAG-66_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:33:27,875] [INFO] Task succeeded: fastANI
[2023-06-17 01:33:27,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:33:27,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:33:27,882] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:33:27,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:33:27,883] [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	82.2778	151	232	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:33:27,885] [INFO] DFAST Taxonomy check result was written to GCA_905620425.1_RIS-SAG-66_genomic.fna/tc_result.tsv
[2023-06-17 01:33:27,886] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:33:27,886] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:33:27,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference/checkm_data
[2023-06-17 01:33:27,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:33:27,899] [INFO] Task started: CheckM
[2023-06-17 01:33:27,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905620425.1_RIS-SAG-66_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905620425.1_RIS-SAG-66_genomic.fna/checkm_input GCA_905620425.1_RIS-SAG-66_genomic.fna/checkm_result
[2023-06-17 01:33:41,911] [INFO] Task succeeded: CheckM
[2023-06-17 01:33:41,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:33:41,932] [INFO] ===== Completeness check finished =====
[2023-06-17 01:33:41,932] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:33:41,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905620425.1_RIS-SAG-66_genomic.fna/markers.fasta)
[2023-06-17 01:33:41,933] [INFO] Task started: Blastn
[2023-06-17 01:33:41,933] [INFO] Running command: blastn -query GCA_905620425.1_RIS-SAG-66_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c63d9a-2d80-441f-a340-4ce87f6c34f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_905620425.1_RIS-SAG-66_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:33:42,715] [INFO] Task succeeded: Blastn
[2023-06-17 01:33:42,719] [INFO] Selected 13 target genomes.
[2023-06-17 01:33:42,719] [INFO] Target genome list was writen to GCA_905620425.1_RIS-SAG-66_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:33:42,720] [INFO] Task started: fastANI
[2023-06-17 01:33:42,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgceb048a7-94a8-405e-8ecb-b068e17aa28b/GCA_905620425.1_RIS-SAG-66_genomic.fna.gz --refList GCA_905620425.1_RIS-SAG-66_genomic.fna/target_genomes_gtdb.txt --output GCA_905620425.1_RIS-SAG-66_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:33:44,935] [INFO] Task succeeded: fastANI
[2023-06-17 01:33:44,951] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:33:44,952] [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_905612495.1	s__Pelagibacter sp905612495	83.6339	99	232	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	83.421	71	232	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	83.376	58	232	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	83.2894	73	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612375.1	s__Pelagibacter sp905612375	82.8592	92	232	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	82.7305	102	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905616395.1	s__Pelagibacter sp905616395	82.7049	137	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.02	95.02	0.70	0.70	2	-
GCA_905618905.1	s__Pelagibacter sp905618905	82.6867	97	232	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	82.2214	89	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612465.1	s__Pelagibacter sp905612465	82.1493	82	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012276695.1	s__Pelagibacter giovannonii	82.0232	154	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932795.1	s__Pelagibacter ubique_S	81.7224	152	232	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014653975.1	s__Pelagibacter sp014653975	80.91	108	232	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 01:33:44,954] [INFO] GTDB search result was written to GCA_905620425.1_RIS-SAG-66_genomic.fna/result_gtdb.tsv
[2023-06-17 01:33:44,954] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:33:44,958] [INFO] DFAST_QC result json was written to GCA_905620425.1_RIS-SAG-66_genomic.fna/dqc_result.json
[2023-06-17 01:33:44,959] [INFO] DFAST_QC completed!
[2023-06-17 01:33:44,959] [INFO] Total running time: 0h0m28s