[2023-06-07 23:54:41,067] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:54:41,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:54:41,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference
[2023-06-07 23:54:43,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:54:43,078] [INFO] Task started: Prodigal
[2023-06-07 23:54:43,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg50de3393-e3bd-45bc-82ce-f90ab0b8f679/GCA_902618565.1_AG-920-C15_genomic.fna.gz | prodigal -d GCA_902618565.1_AG-920-C15_genomic.fna/cds.fna -a GCA_902618565.1_AG-920-C15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:54:44,715] [INFO] Task succeeded: Prodigal
[2023-06-07 23:54:44,715] [INFO] Task started: HMMsearch
[2023-06-07 23:54:44,716] [INFO] Running command: hmmsearch --tblout GCA_902618565.1_AG-920-C15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference/reference_markers.hmm GCA_902618565.1_AG-920-C15_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:54:44,977] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:54:44,978] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg50de3393-e3bd-45bc-82ce-f90ab0b8f679/GCA_902618565.1_AG-920-C15_genomic.fna.gz]
[2023-06-07 23:54:44,993] [INFO] Query marker FASTA was written to GCA_902618565.1_AG-920-C15_genomic.fna/markers.fasta
[2023-06-07 23:54:44,993] [INFO] Task started: Blastn
[2023-06-07 23:54:44,994] [INFO] Running command: blastn -query GCA_902618565.1_AG-920-C15_genomic.fna/markers.fasta -db /var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference/reference_markers.fasta -out GCA_902618565.1_AG-920-C15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:54:47,360] [INFO] Task succeeded: Blastn
[2023-06-07 23:54:47,368] [INFO] Selected 9 target genomes.
[2023-06-07 23:54:47,369] [INFO] Target genome list was writen to GCA_902618565.1_AG-920-C15_genomic.fna/target_genomes.txt
[2023-06-07 23:54:47,371] [INFO] Task started: fastANI
[2023-06-07 23:54:47,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg50de3393-e3bd-45bc-82ce-f90ab0b8f679/GCA_902618565.1_AG-920-C15_genomic.fna.gz --refList GCA_902618565.1_AG-920-C15_genomic.fna/target_genomes.txt --output GCA_902618565.1_AG-920-C15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:54:50,431] [INFO] Task succeeded: fastANI
[2023-06-07 23:54:50,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:54:50,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:54:50,436] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:54:50,436] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:54:50,436] [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	77.7133	105	325	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:54:50,438] [INFO] DFAST Taxonomy check result was written to GCA_902618565.1_AG-920-C15_genomic.fna/tc_result.tsv
[2023-06-07 23:54:50,439] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:54:50,439] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:54:50,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference/checkm_data
[2023-06-07 23:54:50,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:54:50,457] [INFO] Task started: CheckM
[2023-06-07 23:54:50,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902618565.1_AG-920-C15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902618565.1_AG-920-C15_genomic.fna/checkm_input GCA_902618565.1_AG-920-C15_genomic.fna/checkm_result
[2023-06-07 23:55:05,722] [INFO] Task succeeded: CheckM
[2023-06-07 23:55:05,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:55:05,742] [INFO] ===== Completeness check finished =====
[2023-06-07 23:55:05,743] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:55:05,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902618565.1_AG-920-C15_genomic.fna/markers.fasta)
[2023-06-07 23:55:05,744] [INFO] Task started: Blastn
[2023-06-07 23:55:05,744] [INFO] Running command: blastn -query GCA_902618565.1_AG-920-C15_genomic.fna/markers.fasta -db /var/lib/cwl/stg666abd4c-ceab-480f-bd1d-f1e78df13168/dqc_reference/reference_markers_gtdb.fasta -out GCA_902618565.1_AG-920-C15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:55:06,517] [INFO] Task succeeded: Blastn
[2023-06-07 23:55:06,523] [INFO] Selected 21 target genomes.
[2023-06-07 23:55:06,523] [INFO] Target genome list was writen to GCA_902618565.1_AG-920-C15_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:55:06,530] [INFO] Task started: fastANI
[2023-06-07 23:55:06,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg50de3393-e3bd-45bc-82ce-f90ab0b8f679/GCA_902618565.1_AG-920-C15_genomic.fna.gz --refList GCA_902618565.1_AG-920-C15_genomic.fna/target_genomes_gtdb.txt --output GCA_902618565.1_AG-920-C15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:55:11,452] [INFO] Task succeeded: fastANI
[2023-06-07 23:55:11,483] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:55:11,483] [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_902618565.1	s__Pelagibacter sp902618565	100.0	321	325	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_001704065.1	s__Pelagibacter sp001704065	94.2474	270	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.46	95.21	0.83	0.78	7	-
GCA_902615045.1	s__Pelagibacter sp902615045	94.1554	230	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521355.1	s__Pelagibacter sp001704055	94.0325	248	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.10	96.33	0.77	0.72	3	-
GCA_902519325.1	s__Pelagibacter sp902519325	94.012	174	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541285.1	s__Pelagibacter sp902541285	93.9934	234	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902633185.1	s__Pelagibacter sp902633185	93.9823	252	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.35	96.35	0.84	0.84	2	-
GCA_902543575.1	s__Pelagibacter sp902543575	93.8092	252	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.66	97.41	0.82	0.80	3	-
GCA_902618205.1	s__Pelagibacter sp902618205	93.6778	280	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.70	95.67	0.91	0.89	3	-
GCA_902570695.1	s__Pelagibacter sp902570695	93.5133	265	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.72	99.69	0.89	0.86	4	-
GCA_902596975.1	s__Pelagibacter sp902596975	93.485	273	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.65	99.65	0.86	0.86	2	-
GCA_902535625.1	s__Pelagibacter sp902535625	93.4727	196	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613065.1	s__Pelagibacter sp902613065	93.4268	267	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.66	99.66	0.86	0.86	2	-
GCA_902575835.1	s__Pelagibacter sp902575835	93.3116	246	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601895.1	s__Pelagibacter sp902601895	92.0548	212	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524595.1	s__Pelagibacter sp902524595	90.9156	231	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624535.1	s__Pelagibacter sp902624535	90.5281	205	325	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	79.5945	113	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.47	97.47	0.71	0.71	2	-
GCA_902536975.1	s__Pelagibacter sp902536975	78.8087	75	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580945.1	s__Pelagibacter sp902580945	78.7056	147	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216255.1	s__Pelagibacter sp003216255	78.6718	129	325	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.29	95.94	0.82	0.73	4	-
--------------------------------------------------------------------------------
[2023-06-07 23:55:11,485] [INFO] GTDB search result was written to GCA_902618565.1_AG-920-C15_genomic.fna/result_gtdb.tsv
[2023-06-07 23:55:11,486] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:55:11,490] [INFO] DFAST_QC result json was written to GCA_902618565.1_AG-920-C15_genomic.fna/dqc_result.json
[2023-06-07 23:55:11,490] [INFO] DFAST_QC completed!
[2023-06-07 23:55:11,490] [INFO] Total running time: 0h0m30s