[2023-06-08 05:13:33,284] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:13:33,287] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:13:33,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference
[2023-06-08 05:13:35,532] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:13:35,533] [INFO] Task started: Prodigal
[2023-06-08 05:13:35,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b3df7b9-bd40-420a-818b-6d456487214d/GCA_902614705.1_AG-891-M03_genomic.fna.gz | prodigal -d GCA_902614705.1_AG-891-M03_genomic.fna/cds.fna -a GCA_902614705.1_AG-891-M03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:13:37,074] [INFO] Task succeeded: Prodigal
[2023-06-08 05:13:37,075] [INFO] Task started: HMMsearch
[2023-06-08 05:13:37,075] [INFO] Running command: hmmsearch --tblout GCA_902614705.1_AG-891-M03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference/reference_markers.hmm GCA_902614705.1_AG-891-M03_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:13:37,264] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:13:37,266] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4b3df7b9-bd40-420a-818b-6d456487214d/GCA_902614705.1_AG-891-M03_genomic.fna.gz]
[2023-06-08 05:13:37,281] [INFO] Query marker FASTA was written to GCA_902614705.1_AG-891-M03_genomic.fna/markers.fasta
[2023-06-08 05:13:37,282] [INFO] Task started: Blastn
[2023-06-08 05:13:37,282] [INFO] Running command: blastn -query GCA_902614705.1_AG-891-M03_genomic.fna/markers.fasta -db /var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference/reference_markers.fasta -out GCA_902614705.1_AG-891-M03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:13:38,948] [INFO] Task succeeded: Blastn
[2023-06-08 05:13:38,955] [INFO] Selected 8 target genomes.
[2023-06-08 05:13:38,956] [INFO] Target genome list was writen to GCA_902614705.1_AG-891-M03_genomic.fna/target_genomes.txt
[2023-06-08 05:13:38,959] [INFO] Task started: fastANI
[2023-06-08 05:13:38,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3df7b9-bd40-420a-818b-6d456487214d/GCA_902614705.1_AG-891-M03_genomic.fna.gz --refList GCA_902614705.1_AG-891-M03_genomic.fna/target_genomes.txt --output GCA_902614705.1_AG-891-M03_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:13:41,629] [INFO] Task succeeded: fastANI
[2023-06-08 05:13:41,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:13:41,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:13:41,633] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:13:41,633] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:13:41,633] [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
--------------------------------------------------------------------------------
[2023-06-08 05:13:41,635] [INFO] DFAST Taxonomy check result was written to GCA_902614705.1_AG-891-M03_genomic.fna/tc_result.tsv
[2023-06-08 05:13:41,636] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:13:41,636] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:13:41,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference/checkm_data
[2023-06-08 05:13:41,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:13:41,659] [INFO] Task started: CheckM
[2023-06-08 05:13:41,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614705.1_AG-891-M03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614705.1_AG-891-M03_genomic.fna/checkm_input GCA_902614705.1_AG-891-M03_genomic.fna/checkm_result
[2023-06-08 05:13:56,813] [INFO] Task succeeded: CheckM
[2023-06-08 05:13:56,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:13:56,834] [INFO] ===== Completeness check finished =====
[2023-06-08 05:13:56,834] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:13:56,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614705.1_AG-891-M03_genomic.fna/markers.fasta)
[2023-06-08 05:13:56,835] [INFO] Task started: Blastn
[2023-06-08 05:13:56,836] [INFO] Running command: blastn -query GCA_902614705.1_AG-891-M03_genomic.fna/markers.fasta -db /var/lib/cwl/stg78f62672-d503-41f5-b42a-cc3b35a95dc3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614705.1_AG-891-M03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:13:57,274] [INFO] Task succeeded: Blastn
[2023-06-08 05:13:57,278] [INFO] Selected 8 target genomes.
[2023-06-08 05:13:57,278] [INFO] Target genome list was writen to GCA_902614705.1_AG-891-M03_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:13:57,279] [INFO] Task started: fastANI
[2023-06-08 05:13:57,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3df7b9-bd40-420a-818b-6d456487214d/GCA_902614705.1_AG-891-M03_genomic.fna.gz --refList GCA_902614705.1_AG-891-M03_genomic.fna/target_genomes_gtdb.txt --output GCA_902614705.1_AG-891-M03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:13:59,123] [INFO] Task succeeded: fastANI
[2023-06-08 05:13:59,138] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 05:13:59,139] [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_902612915.1	s__SAR86A sp902612915	97.2081	217	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.80	95.61	0.84	0.75	10	inconclusive
GCA_004212975.1	s__SAR86A sp004212975	95.1782	177	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.30	95.02	0.85	0.76	8	inconclusive
GCA_902617045.1	s__SAR86A sp902617045	94.4477	230	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.06	95.32	0.86	0.86	4	-
GCA_902541175.1	s__SAR86A sp902541175	94.1447	233	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.65	95.31	0.89	0.85	3	-
GCA_902547295.1	s__SAR86A sp902547295	94.0595	216	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591925.1	s__SAR86A sp902591925	90.6143	223	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	97.32	97.27	0.90	0.89	3	-
GCA_902631785.1	s__SAR86A sp902631785	83.9609	183	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.84	96.84	0.79	0.79	2	-
GCA_000252525.1	s__SAR86A sp000252525	83.3724	142	276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SAR86A	95.0	96.49	95.25	0.88	0.84	16	-
--------------------------------------------------------------------------------
[2023-06-08 05:13:59,141] [INFO] GTDB search result was written to GCA_902614705.1_AG-891-M03_genomic.fna/result_gtdb.tsv
[2023-06-08 05:13:59,141] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:13:59,145] [INFO] DFAST_QC result json was written to GCA_902614705.1_AG-891-M03_genomic.fna/dqc_result.json
[2023-06-08 05:13:59,145] [INFO] DFAST_QC completed!
[2023-06-08 05:13:59,146] [INFO] Total running time: 0h0m26s