[2023-06-08 15:29:54,485] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:29:54,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:29:54,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference
[2023-06-08 15:29:55,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:29:55,641] [INFO] Task started: Prodigal
[2023-06-08 15:29:55,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg04d26420-db3a-411a-b37d-aca75ec537d7/GCA_902528455.1_AG-896-J21_genomic.fna.gz | prodigal -d GCA_902528455.1_AG-896-J21_genomic.fna/cds.fna -a GCA_902528455.1_AG-896-J21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:29:58,192] [INFO] Task succeeded: Prodigal
[2023-06-08 15:29:58,192] [INFO] Task started: HMMsearch
[2023-06-08 15:29:58,192] [INFO] Running command: hmmsearch --tblout GCA_902528455.1_AG-896-J21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference/reference_markers.hmm GCA_902528455.1_AG-896-J21_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:29:58,322] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:29:58,323] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg04d26420-db3a-411a-b37d-aca75ec537d7/GCA_902528455.1_AG-896-J21_genomic.fna.gz]
[2023-06-08 15:29:58,335] [INFO] Query marker FASTA was written to GCA_902528455.1_AG-896-J21_genomic.fna/markers.fasta
[2023-06-08 15:29:58,336] [INFO] Task started: Blastn
[2023-06-08 15:29:58,336] [INFO] Running command: blastn -query GCA_902528455.1_AG-896-J21_genomic.fna/markers.fasta -db /var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference/reference_markers.fasta -out GCA_902528455.1_AG-896-J21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:29:58,842] [INFO] Task succeeded: Blastn
[2023-06-08 15:29:58,846] [INFO] Selected 15 target genomes.
[2023-06-08 15:29:58,847] [INFO] Target genome list was writen to GCA_902528455.1_AG-896-J21_genomic.fna/target_genomes.txt
[2023-06-08 15:29:58,847] [INFO] Task started: fastANI
[2023-06-08 15:29:58,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d26420-db3a-411a-b37d-aca75ec537d7/GCA_902528455.1_AG-896-J21_genomic.fna.gz --refList GCA_902528455.1_AG-896-J21_genomic.fna/target_genomes.txt --output GCA_902528455.1_AG-896-J21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:30:03,033] [INFO] Task succeeded: fastANI
[2023-06-08 15:30:03,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:30:03,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:30:03,037] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:30:03,037] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:30:03,037] [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	77.5305	101	280	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:30:03,039] [INFO] DFAST Taxonomy check result was written to GCA_902528455.1_AG-896-J21_genomic.fna/tc_result.tsv
[2023-06-08 15:30:03,039] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:30:03,040] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:30:03,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference/checkm_data
[2023-06-08 15:30:03,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:30:03,052] [INFO] Task started: CheckM
[2023-06-08 15:30:03,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902528455.1_AG-896-J21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902528455.1_AG-896-J21_genomic.fna/checkm_input GCA_902528455.1_AG-896-J21_genomic.fna/checkm_result
[2023-06-08 15:30:17,501] [INFO] Task succeeded: CheckM
[2023-06-08 15:30:17,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:30:17,522] [INFO] ===== Completeness check finished =====
[2023-06-08 15:30:17,523] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:30:17,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902528455.1_AG-896-J21_genomic.fna/markers.fasta)
[2023-06-08 15:30:17,523] [INFO] Task started: Blastn
[2023-06-08 15:30:17,523] [INFO] Running command: blastn -query GCA_902528455.1_AG-896-J21_genomic.fna/markers.fasta -db /var/lib/cwl/stg3746c522-849f-4344-bc00-868512a4a44a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902528455.1_AG-896-J21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:30:18,267] [INFO] Task succeeded: Blastn
[2023-06-08 15:30:18,271] [INFO] Selected 12 target genomes.
[2023-06-08 15:30:18,271] [INFO] Target genome list was writen to GCA_902528455.1_AG-896-J21_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:30:18,275] [INFO] Task started: fastANI
[2023-06-08 15:30:18,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d26420-db3a-411a-b37d-aca75ec537d7/GCA_902528455.1_AG-896-J21_genomic.fna.gz --refList GCA_902528455.1_AG-896-J21_genomic.fna/target_genomes_gtdb.txt --output GCA_902528455.1_AG-896-J21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:30:20,743] [INFO] Task succeeded: fastANI
[2023-06-08 15:30:20,753] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:30:20,753] [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_902634885.1	s__Pelagibacter sp902634885	97.6237	212	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.47	97.62	0.77	0.76	3	conclusive
GCA_902634935.1	s__Pelagibacter sp902634935	94.8096	211	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616205.1	s__Pelagibacter sp902616205	94.2654	158	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601315.1	s__Pelagibacter sp902601315	93.5083	215	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546765.1	s__Pelagibacter sp902546765	93.2895	164	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.47	97.47	0.71	0.71	2	-
GCA_902576045.1	s__Pelagibacter sp902576045	93.0105	193	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.81	95.50	0.75	0.71	6	-
GCF_002101295.1	s__Pelagibacter sp002101295	92.6112	249	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.60	0.92	0.90	4	-
GCA_902614125.1	s__Pelagibacter sp902614125	92.1178	211	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592445.1	s__Pelagibacter sp902592445	91.9809	199	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.56	95.56	0.78	0.78	2	-
GCA_902625715.1	s__Pelagibacter sp902625715	90.7003	196	280	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.20	95.77	0.80	0.79	3	-
GCA_902581445.1	s__Pelagibacter sp902581445	78.1643	81	280	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 15:30:20,755] [INFO] GTDB search result was written to GCA_902528455.1_AG-896-J21_genomic.fna/result_gtdb.tsv
[2023-06-08 15:30:20,756] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:30:20,758] [INFO] DFAST_QC result json was written to GCA_902528455.1_AG-896-J21_genomic.fna/dqc_result.json
[2023-06-08 15:30:20,758] [INFO] DFAST_QC completed!
[2023-06-08 15:30:20,758] [INFO] Total running time: 0h0m26s