[2023-06-04 23:12:16,546] [INFO] DFAST_QC pipeline started.
[2023-06-04 23:12:16,548] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 23:12:16,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference
[2023-06-04 23:12:17,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 23:12:17,817] [INFO] Task started: Prodigal
[2023-06-04 23:12:17,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg99051cfe-24b9-4ac6-b820-77bc5c368c8b/GCA_902524635.1_AG-337-D19_genomic.fna.gz | prodigal -d GCA_902524635.1_AG-337-D19_genomic.fna/cds.fna -a GCA_902524635.1_AG-337-D19_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 23:12:20,431] [INFO] Task succeeded: Prodigal
[2023-06-04 23:12:20,432] [INFO] Task started: HMMsearch
[2023-06-04 23:12:20,432] [INFO] Running command: hmmsearch --tblout GCA_902524635.1_AG-337-D19_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference/reference_markers.hmm GCA_902524635.1_AG-337-D19_genomic.fna/protein.faa > /dev/null
[2023-06-04 23:12:20,641] [INFO] Task succeeded: HMMsearch
[2023-06-04 23:12:20,643] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg99051cfe-24b9-4ac6-b820-77bc5c368c8b/GCA_902524635.1_AG-337-D19_genomic.fna.gz]
[2023-06-04 23:12:20,658] [INFO] Query marker FASTA was written to GCA_902524635.1_AG-337-D19_genomic.fna/markers.fasta
[2023-06-04 23:12:20,659] [INFO] Task started: Blastn
[2023-06-04 23:12:20,659] [INFO] Running command: blastn -query GCA_902524635.1_AG-337-D19_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference/reference_markers.fasta -out GCA_902524635.1_AG-337-D19_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:21,199] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:21,205] [INFO] Selected 6 target genomes.
[2023-06-04 23:12:21,205] [INFO] Target genome list was writen to GCA_902524635.1_AG-337-D19_genomic.fna/target_genomes.txt
[2023-06-04 23:12:21,207] [INFO] Task started: fastANI
[2023-06-04 23:12:21,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg99051cfe-24b9-4ac6-b820-77bc5c368c8b/GCA_902524635.1_AG-337-D19_genomic.fna.gz --refList GCA_902524635.1_AG-337-D19_genomic.fna/target_genomes.txt --output GCA_902524635.1_AG-337-D19_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 23:12:23,456] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:23,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 23:12:23,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 23:12:23,461] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 23:12:23,461] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 23:12:23,461] [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	77.7681	100	279	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 23:12:23,463] [INFO] DFAST Taxonomy check result was written to GCA_902524635.1_AG-337-D19_genomic.fna/tc_result.tsv
[2023-06-04 23:12:23,464] [INFO] ===== Taxonomy check completed =====
[2023-06-04 23:12:23,464] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 23:12:23,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference/checkm_data
[2023-06-04 23:12:23,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 23:12:23,482] [INFO] Task started: CheckM
[2023-06-04 23:12:23,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902524635.1_AG-337-D19_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902524635.1_AG-337-D19_genomic.fna/checkm_input GCA_902524635.1_AG-337-D19_genomic.fna/checkm_result
[2023-06-04 23:12:39,585] [INFO] Task succeeded: CheckM
[2023-06-04 23:12:39,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 23:12:39,607] [INFO] ===== Completeness check finished =====
[2023-06-04 23:12:39,608] [INFO] ===== Start GTDB Search =====
[2023-06-04 23:12:39,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902524635.1_AG-337-D19_genomic.fna/markers.fasta)
[2023-06-04 23:12:39,608] [INFO] Task started: Blastn
[2023-06-04 23:12:39,609] [INFO] Running command: blastn -query GCA_902524635.1_AG-337-D19_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b55a6fc-ced0-496d-a881-78aa7bfcb7c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902524635.1_AG-337-D19_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 23:12:40,402] [INFO] Task succeeded: Blastn
[2023-06-04 23:12:40,406] [INFO] Selected 15 target genomes.
[2023-06-04 23:12:40,406] [INFO] Target genome list was writen to GCA_902524635.1_AG-337-D19_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 23:12:40,414] [INFO] Task started: fastANI
[2023-06-04 23:12:40,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg99051cfe-24b9-4ac6-b820-77bc5c368c8b/GCA_902524635.1_AG-337-D19_genomic.fna.gz --refList GCA_902524635.1_AG-337-D19_genomic.fna/target_genomes_gtdb.txt --output GCA_902524635.1_AG-337-D19_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 23:12:43,982] [INFO] Task succeeded: fastANI
[2023-06-04 23:12:43,994] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 23:12:43,994] [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_902524635.1	s__Pelagibacter sp902524635	100.0	277	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902522365.1	s__Pelagibacter sp902522365	91.5776	155	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516395.1	s__Pelagibacter sp902516395	91.3773	190	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517495.1	s__Pelagibacter sp902517495	91.109	184	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611465.1	s__Pelagibacter sp902611465	90.9157	192	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594335.1	s__Pelagibacter sp902594335	90.7203	211	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592715.1	s__Pelagibacter sp902592715	90.5481	202	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902609535.1	s__Pelagibacter sp902609535	90.4849	185	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902570545.1	s__Pelagibacter sp902570545	90.3958	120	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520695.1	s__Pelagibacter sp902520695	89.306	224	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902555275.1	s__Pelagibacter sp902555275	89.1752	205	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.10	98.10	0.78	0.78	2	-
GCA_014654115.1	s__Pelagibacter sp014654115	87.4339	145	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902549785.1	s__Pelagibacter sp902549785	86.4346	133	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.65	95.65	0.64	0.64	2	-
GCA_902629935.1	s__Pelagibacter sp902629935	77.6613	113	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 23:12:43,996] [INFO] GTDB search result was written to GCA_902524635.1_AG-337-D19_genomic.fna/result_gtdb.tsv
[2023-06-04 23:12:43,997] [INFO] ===== GTDB Search completed =====
[2023-06-04 23:12:44,000] [INFO] DFAST_QC result json was written to GCA_902524635.1_AG-337-D19_genomic.fna/dqc_result.json
[2023-06-04 23:12:44,000] [INFO] DFAST_QC completed!
[2023-06-04 23:12:44,000] [INFO] Total running time: 0h0m27s