[2023-06-08 12:18:49,803] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:18:49,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:18:49,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference
[2023-06-08 12:18:51,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:18:51,003] [INFO] Task started: Prodigal
[2023-06-08 12:18:51,004] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ca50eef-911a-4279-a6c8-7bd95ea126a4/GCA_902614165.1_AG-918-P15_genomic.fna.gz | prodigal -d GCA_902614165.1_AG-918-P15_genomic.fna/cds.fna -a GCA_902614165.1_AG-918-P15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:18:53,611] [INFO] Task succeeded: Prodigal
[2023-06-08 12:18:53,612] [INFO] Task started: HMMsearch
[2023-06-08 12:18:53,612] [INFO] Running command: hmmsearch --tblout GCA_902614165.1_AG-918-P15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference/reference_markers.hmm GCA_902614165.1_AG-918-P15_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:18:53,757] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:18:53,758] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4ca50eef-911a-4279-a6c8-7bd95ea126a4/GCA_902614165.1_AG-918-P15_genomic.fna.gz]
[2023-06-08 12:18:53,773] [INFO] Query marker FASTA was written to GCA_902614165.1_AG-918-P15_genomic.fna/markers.fasta
[2023-06-08 12:18:53,774] [INFO] Task started: Blastn
[2023-06-08 12:18:53,774] [INFO] Running command: blastn -query GCA_902614165.1_AG-918-P15_genomic.fna/markers.fasta -db /var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference/reference_markers.fasta -out GCA_902614165.1_AG-918-P15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:18:54,247] [INFO] Task succeeded: Blastn
[2023-06-08 12:18:54,251] [INFO] Selected 11 target genomes.
[2023-06-08 12:18:54,251] [INFO] Target genome list was writen to GCA_902614165.1_AG-918-P15_genomic.fna/target_genomes.txt
[2023-06-08 12:18:54,253] [INFO] Task started: fastANI
[2023-06-08 12:18:54,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca50eef-911a-4279-a6c8-7bd95ea126a4/GCA_902614165.1_AG-918-P15_genomic.fna.gz --refList GCA_902614165.1_AG-918-P15_genomic.fna/target_genomes.txt --output GCA_902614165.1_AG-918-P15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:18:58,438] [INFO] Task succeeded: fastANI
[2023-06-08 12:18:58,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:18:58,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:18:58,447] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:18:58,447] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:18:58,447] [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	78.5953	155	297	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:18:58,449] [INFO] DFAST Taxonomy check result was written to GCA_902614165.1_AG-918-P15_genomic.fna/tc_result.tsv
[2023-06-08 12:18:58,449] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:18:58,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:18:58,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference/checkm_data
[2023-06-08 12:18:58,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:18:58,470] [INFO] Task started: CheckM
[2023-06-08 12:18:58,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614165.1_AG-918-P15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614165.1_AG-918-P15_genomic.fna/checkm_input GCA_902614165.1_AG-918-P15_genomic.fna/checkm_result
[2023-06-08 12:19:14,489] [INFO] Task succeeded: CheckM
[2023-06-08 12:19:14,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:19:14,510] [INFO] ===== Completeness check finished =====
[2023-06-08 12:19:14,511] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:19:14,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614165.1_AG-918-P15_genomic.fna/markers.fasta)
[2023-06-08 12:19:14,511] [INFO] Task started: Blastn
[2023-06-08 12:19:14,511] [INFO] Running command: blastn -query GCA_902614165.1_AG-918-P15_genomic.fna/markers.fasta -db /var/lib/cwl/stg5576b7cb-bef7-49e8-a475-0100d2912559/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614165.1_AG-918-P15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:15,053] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:15,057] [INFO] Selected 15 target genomes.
[2023-06-08 12:19:15,057] [INFO] Target genome list was writen to GCA_902614165.1_AG-918-P15_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:19:15,062] [INFO] Task started: fastANI
[2023-06-08 12:19:15,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca50eef-911a-4279-a6c8-7bd95ea126a4/GCA_902614165.1_AG-918-P15_genomic.fna.gz --refList GCA_902614165.1_AG-918-P15_genomic.fna/target_genomes_gtdb.txt --output GCA_902614165.1_AG-918-P15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:19:18,197] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:18,209] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:19:18,210] [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
GCF_001179925.1	s__Pelagibacter ubique_E	98.8927	225	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.89	98.89	0.76	0.76	2	conclusive
GCA_902517735.1	s__Pelagibacter sp902517735	84.1244	132	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578525.1	s__Pelagibacter sp902578525	82.6244	183	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578775.1	s__Pelagibacter sp902578775	82.113	204	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607945.1	s__Pelagibacter sp902607945	82.021	138	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654245.1	s__Pelagibacter sp014654245	81.7683	118	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622805.1	s__Pelagibacter sp902622805	81.6585	168	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.81	99.81	0.79	0.79	2	-
GCA_902571235.1	s__Pelagibacter sp902571235	81.6535	145	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902555945.1	s__Pelagibacter sp902555945	81.5278	193	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522895.1	s__Pelagibacter sp902522895	81.4805	96	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594235.1	s__Pelagibacter sp902594235	81.3379	199	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278065.1	s__Pelagibacter sp003278065	81.1961	177	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001179885.1	s__Pelagibacter ubique_N	81.1521	95	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177485.1	s__Pelagibacter sp900177485	79.529	191	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902552705.1	s__Pelagibacter sp902552705	79.2933	116	297	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:19:18,212] [INFO] GTDB search result was written to GCA_902614165.1_AG-918-P15_genomic.fna/result_gtdb.tsv
[2023-06-08 12:19:18,212] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:19:18,216] [INFO] DFAST_QC result json was written to GCA_902614165.1_AG-918-P15_genomic.fna/dqc_result.json
[2023-06-08 12:19:18,216] [INFO] DFAST_QC completed!
[2023-06-08 12:19:18,216] [INFO] Total running time: 0h0m28s