[2023-06-17 11:44:13,973] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:13,976] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:13,976] [INFO] DQC Reference Directory: /var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference
[2023-06-17 11:44:17,172] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:17,173] [INFO] Task started: Prodigal
[2023-06-17 11:44:17,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ceeac53-f7ad-4de7-9679-b7e61bf34232/GCA_013205255.1_ASM1320525v1_genomic.fna.gz | prodigal -d GCA_013205255.1_ASM1320525v1_genomic.fna/cds.fna -a GCA_013205255.1_ASM1320525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:30,602] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:30,602] [INFO] Task started: HMMsearch
[2023-06-17 11:44:30,602] [INFO] Running command: hmmsearch --tblout GCA_013205255.1_ASM1320525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference/reference_markers.hmm GCA_013205255.1_ASM1320525v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:30,806] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:30,807] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ceeac53-f7ad-4de7-9679-b7e61bf34232/GCA_013205255.1_ASM1320525v1_genomic.fna.gz]
[2023-06-17 11:44:30,850] [INFO] Query marker FASTA was written to GCA_013205255.1_ASM1320525v1_genomic.fna/markers.fasta
[2023-06-17 11:44:30,851] [INFO] Task started: Blastn
[2023-06-17 11:44:30,851] [INFO] Running command: blastn -query GCA_013205255.1_ASM1320525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference/reference_markers.fasta -out GCA_013205255.1_ASM1320525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:31,549] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:31,554] [INFO] Selected 25 target genomes.
[2023-06-17 11:44:31,554] [INFO] Target genome list was writen to GCA_013205255.1_ASM1320525v1_genomic.fna/target_genomes.txt
[2023-06-17 11:44:31,556] [INFO] Task started: fastANI
[2023-06-17 11:44:31,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ceeac53-f7ad-4de7-9679-b7e61bf34232/GCA_013205255.1_ASM1320525v1_genomic.fna.gz --refList GCA_013205255.1_ASM1320525v1_genomic.fna/target_genomes.txt --output GCA_013205255.1_ASM1320525v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:44:48,342] [INFO] Task succeeded: fastANI
[2023-06-17 11:44:48,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:44:48,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:44:48,349] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:44:48,349] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:44:48,349] [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
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	77.4621	67	517	95	below_threshold
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.2687	128	517	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	74.8764	54	517	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:44:48,351] [INFO] DFAST Taxonomy check result was written to GCA_013205255.1_ASM1320525v1_genomic.fna/tc_result.tsv
[2023-06-17 11:44:48,352] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:44:48,352] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:44:48,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference/checkm_data
[2023-06-17 11:44:48,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:44:48,385] [INFO] Task started: CheckM
[2023-06-17 11:44:48,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013205255.1_ASM1320525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013205255.1_ASM1320525v1_genomic.fna/checkm_input GCA_013205255.1_ASM1320525v1_genomic.fna/checkm_result
[2023-06-17 11:45:28,378] [INFO] Task succeeded: CheckM
[2023-06-17 11:45:28,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 11:45:28,404] [INFO] ===== Completeness check finished =====
[2023-06-17 11:45:28,404] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:45:28,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013205255.1_ASM1320525v1_genomic.fna/markers.fasta)
[2023-06-17 11:45:28,405] [INFO] Task started: Blastn
[2023-06-17 11:45:28,405] [INFO] Running command: blastn -query GCA_013205255.1_ASM1320525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2d6ea6c-9136-4639-955b-dbce0434d4c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_013205255.1_ASM1320525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:45:29,285] [INFO] Task succeeded: Blastn
[2023-06-17 11:45:29,290] [INFO] Selected 10 target genomes.
[2023-06-17 11:45:29,290] [INFO] Target genome list was writen to GCA_013205255.1_ASM1320525v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:45:29,296] [INFO] Task started: fastANI
[2023-06-17 11:45:29,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ceeac53-f7ad-4de7-9679-b7e61bf34232/GCA_013205255.1_ASM1320525v1_genomic.fna.gz --refList GCA_013205255.1_ASM1320525v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013205255.1_ASM1320525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:45:33,753] [INFO] Task succeeded: fastANI
[2023-06-17 11:45:33,766] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:45:33,767] [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	99.9999	503	517	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	94.183	409	517	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	83.6943	222	517	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	83.5636	313	517	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	83.4659	326	517	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	82.4802	307	517	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	80.1909	130	517	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_002252675.1	s__Cyanobium sp002252675	79.9652	260	517	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCA_016882545.1	s__Vulcanococcus sp016882545	79.7706	186	517	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249115.1	s__QBMD01 sp003249115	78.7407	212	517	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-17 11:45:33,768] [INFO] GTDB search result was written to GCA_013205255.1_ASM1320525v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:45:33,769] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:45:33,772] [INFO] DFAST_QC result json was written to GCA_013205255.1_ASM1320525v1_genomic.fna/dqc_result.json
[2023-06-17 11:45:33,772] [INFO] DFAST_QC completed!
[2023-06-17 11:45:33,772] [INFO] Total running time: 0h1m20s