[2023-06-08 00:35:08,492] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:35:08,495] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:35:08,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference
[2023-06-08 00:35:10,011] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:35:10,015] [INFO] Task started: Prodigal
[2023-06-08 00:35:10,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgceadda38-f3fa-49c3-9db3-dc773f548426/GCA_902528885.1_AG-896-L17_genomic.fna.gz | prodigal -d GCA_902528885.1_AG-896-L17_genomic.fna/cds.fna -a GCA_902528885.1_AG-896-L17_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:12,744] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:12,744] [INFO] Task started: HMMsearch
[2023-06-08 00:35:12,745] [INFO] Running command: hmmsearch --tblout GCA_902528885.1_AG-896-L17_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference/reference_markers.hmm GCA_902528885.1_AG-896-L17_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:12,957] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:12,958] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgceadda38-f3fa-49c3-9db3-dc773f548426/GCA_902528885.1_AG-896-L17_genomic.fna.gz]
[2023-06-08 00:35:12,978] [INFO] Query marker FASTA was written to GCA_902528885.1_AG-896-L17_genomic.fna/markers.fasta
[2023-06-08 00:35:12,978] [INFO] Task started: Blastn
[2023-06-08 00:35:12,978] [INFO] Running command: blastn -query GCA_902528885.1_AG-896-L17_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference/reference_markers.fasta -out GCA_902528885.1_AG-896-L17_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:13,554] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:13,558] [INFO] Selected 11 target genomes.
[2023-06-08 00:35:13,558] [INFO] Target genome list was writen to GCA_902528885.1_AG-896-L17_genomic.fna/target_genomes.txt
[2023-06-08 00:35:13,561] [INFO] Task started: fastANI
[2023-06-08 00:35:13,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgceadda38-f3fa-49c3-9db3-dc773f548426/GCA_902528885.1_AG-896-L17_genomic.fna.gz --refList GCA_902528885.1_AG-896-L17_genomic.fna/target_genomes.txt --output GCA_902528885.1_AG-896-L17_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:16,616] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:16,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:16,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:16,621] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:16,621] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:35:16,621] [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	78.1152	127	295	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:35:16,623] [INFO] DFAST Taxonomy check result was written to GCA_902528885.1_AG-896-L17_genomic.fna/tc_result.tsv
[2023-06-08 00:35:16,623] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:16,624] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:16,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference/checkm_data
[2023-06-08 00:35:16,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:16,642] [INFO] Task started: CheckM
[2023-06-08 00:35:16,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902528885.1_AG-896-L17_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902528885.1_AG-896-L17_genomic.fna/checkm_input GCA_902528885.1_AG-896-L17_genomic.fna/checkm_result
[2023-06-08 00:35:33,464] [INFO] Task succeeded: CheckM
[2023-06-08 00:35:33,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:35:33,493] [INFO] ===== Completeness check finished =====
[2023-06-08 00:35:33,494] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:35:33,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902528885.1_AG-896-L17_genomic.fna/markers.fasta)
[2023-06-08 00:35:33,495] [INFO] Task started: Blastn
[2023-06-08 00:35:33,495] [INFO] Running command: blastn -query GCA_902528885.1_AG-896-L17_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f36ed7e-5e4f-43c7-bc37-6932672e6262/dqc_reference/reference_markers_gtdb.fasta -out GCA_902528885.1_AG-896-L17_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:34,368] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:34,371] [INFO] Selected 12 target genomes.
[2023-06-08 00:35:34,372] [INFO] Target genome list was writen to GCA_902528885.1_AG-896-L17_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:35:34,378] [INFO] Task started: fastANI
[2023-06-08 00:35:34,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgceadda38-f3fa-49c3-9db3-dc773f548426/GCA_902528885.1_AG-896-L17_genomic.fna.gz --refList GCA_902528885.1_AG-896-L17_genomic.fna/target_genomes_gtdb.txt --output GCA_902528885.1_AG-896-L17_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:35:36,935] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:36,945] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:35:36,946] [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_902576335.1	s__Pelagibacter sp902576335	99.8968	238	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.90	99.90	0.81	0.81	2	conclusive
GCA_902618485.1	s__Pelagibacter sp902618485	94.2366	236	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.24	98.89	0.85	0.83	4	-
GCA_902538495.1	s__Pelagibacter sp902538495	94.2133	218	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.93	99.93	0.77	0.77	2	-
GCA_902620465.1	s__Pelagibacter sp902620465	94.1352	231	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.02	95.02	0.74	0.74	2	-
GCA_902544135.1	s__Pelagibacter sp902544135	93.5698	260	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.90	99.90	0.91	0.91	2	-
GCA_902615145.1	s__Pelagibacter sp902615145	93.5439	187	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.53	99.53	0.73	0.73	2	-
GCA_902537895.1	s__Pelagibacter sp902537895	93.4181	215	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524345.1	s__Pelagibacter sp902524345	92.8483	256	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.38	99.08	0.90	0.86	4	-
GCA_902597575.1	s__Pelagibacter sp902597575	92.566	147	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539145.1	s__Pelagibacter sp902539145	92.0974	135	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563555.1	s__Pelagibacter sp902563555	91.2819	200	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.38	99.38	0.73	0.73	2	-
GCA_902541315.1	s__Pelagibacter sp902541315	90.7131	208	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.70	95.61	0.75	0.72	3	-
--------------------------------------------------------------------------------
[2023-06-08 00:35:36,948] [INFO] GTDB search result was written to GCA_902528885.1_AG-896-L17_genomic.fna/result_gtdb.tsv
[2023-06-08 00:35:36,948] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:35:36,952] [INFO] DFAST_QC result json was written to GCA_902528885.1_AG-896-L17_genomic.fna/dqc_result.json
[2023-06-08 00:35:36,952] [INFO] DFAST_QC completed!
[2023-06-08 00:35:36,953] [INFO] Total running time: 0h0m28s