[2023-06-07 22:13:47,082] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:13:47,085] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:13:47,085] [INFO] DQC Reference Directory: /var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference
[2023-06-07 22:13:48,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:13:48,463] [INFO] Task started: Prodigal
[2023-06-07 22:13:48,464] [INFO] Running command: gunzip -c /var/lib/cwl/stga2cf667f-fc19-407c-8c49-e27e2827d2b9/GCA_945863245.1_MoE-02may19-238_genomic.fna.gz | prodigal -d GCA_945863245.1_MoE-02may19-238_genomic.fna/cds.fna -a GCA_945863245.1_MoE-02may19-238_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:14:03,418] [INFO] Task succeeded: Prodigal
[2023-06-07 22:14:03,418] [INFO] Task started: HMMsearch
[2023-06-07 22:14:03,419] [INFO] Running command: hmmsearch --tblout GCA_945863245.1_MoE-02may19-238_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference/reference_markers.hmm GCA_945863245.1_MoE-02may19-238_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:14:03,662] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:14:03,664] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga2cf667f-fc19-407c-8c49-e27e2827d2b9/GCA_945863245.1_MoE-02may19-238_genomic.fna.gz]
[2023-06-07 22:14:03,700] [INFO] Query marker FASTA was written to GCA_945863245.1_MoE-02may19-238_genomic.fna/markers.fasta
[2023-06-07 22:14:03,701] [INFO] Task started: Blastn
[2023-06-07 22:14:03,701] [INFO] Running command: blastn -query GCA_945863245.1_MoE-02may19-238_genomic.fna/markers.fasta -db /var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference/reference_markers.fasta -out GCA_945863245.1_MoE-02may19-238_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:14:04,305] [INFO] Task succeeded: Blastn
[2023-06-07 22:14:04,312] [INFO] Selected 24 target genomes.
[2023-06-07 22:14:04,313] [INFO] Target genome list was writen to GCA_945863245.1_MoE-02may19-238_genomic.fna/target_genomes.txt
[2023-06-07 22:14:04,316] [INFO] Task started: fastANI
[2023-06-07 22:14:04,317] [INFO] Running command: fastANI --query /var/lib/cwl/stga2cf667f-fc19-407c-8c49-e27e2827d2b9/GCA_945863245.1_MoE-02may19-238_genomic.fna.gz --refList GCA_945863245.1_MoE-02may19-238_genomic.fna/target_genomes.txt --output GCA_945863245.1_MoE-02may19-238_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:14:19,956] [INFO] Task succeeded: fastANI
[2023-06-07 22:14:19,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:14:19,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:14:19,961] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:14:19,961] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:14:19,961] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	78.0587	208	774	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	77.01	98	774	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:14:19,964] [INFO] DFAST Taxonomy check result was written to GCA_945863245.1_MoE-02may19-238_genomic.fna/tc_result.tsv
[2023-06-07 22:14:19,965] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:14:19,965] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:14:19,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference/checkm_data
[2023-06-07 22:14:19,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:14:19,997] [INFO] Task started: CheckM
[2023-06-07 22:14:19,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945863245.1_MoE-02may19-238_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945863245.1_MoE-02may19-238_genomic.fna/checkm_input GCA_945863245.1_MoE-02may19-238_genomic.fna/checkm_result
[2023-06-07 22:15:03,114] [INFO] Task succeeded: CheckM
[2023-06-07 22:15:03,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:15:03,141] [INFO] ===== Completeness check finished =====
[2023-06-07 22:15:03,141] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:15:03,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945863245.1_MoE-02may19-238_genomic.fna/markers.fasta)
[2023-06-07 22:15:03,142] [INFO] Task started: Blastn
[2023-06-07 22:15:03,142] [INFO] Running command: blastn -query GCA_945863245.1_MoE-02may19-238_genomic.fna/markers.fasta -db /var/lib/cwl/stge6763f2c-b8c2-4d88-a935-7d23c16c856e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945863245.1_MoE-02may19-238_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:15:03,972] [INFO] Task succeeded: Blastn
[2023-06-07 22:15:03,977] [INFO] Selected 11 target genomes.
[2023-06-07 22:15:03,977] [INFO] Target genome list was writen to GCA_945863245.1_MoE-02may19-238_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:15:03,984] [INFO] Task started: fastANI
[2023-06-07 22:15:03,985] [INFO] Running command: fastANI --query /var/lib/cwl/stga2cf667f-fc19-407c-8c49-e27e2827d2b9/GCA_945863245.1_MoE-02may19-238_genomic.fna.gz --refList GCA_945863245.1_MoE-02may19-238_genomic.fna/target_genomes_gtdb.txt --output GCA_945863245.1_MoE-02may19-238_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:15:10,289] [INFO] Task succeeded: fastANI
[2023-06-07 22:15:10,310] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:15:10,311] [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_013205255.1	s__Cyanobium_A sp013205255	95.6383	341	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015840335.1	s__Cyanobium_A sp015840335	94.8768	664	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697415.1	s__Cyanobium_A sp014697415	83.9081	543	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882385.1	s__Cyanobium_A sp016882385	83.8298	384	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252665.1	s__Cyanobium_A sp002252665	83.5391	546	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011885.1	s__Cyanobium_A usitatum	82.9334	500	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882415.1	s__Vulcanococcus sp016882415	81.2585	242	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088535.1	s__NIES-981 sp900088535	80.833	470	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252675.1	s__Cyanobium sp002252675	80.4484	459	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCF_002252635.1	s__MW101C3 sp002252635	79.5671	384	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__MW101C3	95.0	97.20	97.20	0.89	0.89	2	-
GCA_003249115.1	s__QBMD01 sp003249115	79.1128	369	774	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-07 22:15:10,313] [INFO] GTDB search result was written to GCA_945863245.1_MoE-02may19-238_genomic.fna/result_gtdb.tsv
[2023-06-07 22:15:10,314] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:15:10,317] [INFO] DFAST_QC result json was written to GCA_945863245.1_MoE-02may19-238_genomic.fna/dqc_result.json
[2023-06-07 22:15:10,318] [INFO] DFAST_QC completed!
[2023-06-07 22:15:10,318] [INFO] Total running time: 0h1m23s