[2023-06-18 19:17:37,237] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:17:37,241] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:17:37,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference
[2023-06-18 19:17:38,513] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:17:38,514] [INFO] Task started: Prodigal
[2023-06-18 19:17:38,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg715e89f7-3626-4f95-88e1-442b8c256ca0/GCA_018607185.1_ASM1860718v1_genomic.fna.gz | prodigal -d GCA_018607185.1_ASM1860718v1_genomic.fna/cds.fna -a GCA_018607185.1_ASM1860718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:17:50,926] [INFO] Task succeeded: Prodigal
[2023-06-18 19:17:50,927] [INFO] Task started: HMMsearch
[2023-06-18 19:17:50,927] [INFO] Running command: hmmsearch --tblout GCA_018607185.1_ASM1860718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference/reference_markers.hmm GCA_018607185.1_ASM1860718v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:17:51,178] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:17:51,179] [INFO] Found 6/6 markers.
[2023-06-18 19:17:51,204] [INFO] Query marker FASTA was written to GCA_018607185.1_ASM1860718v1_genomic.fna/markers.fasta
[2023-06-18 19:17:51,204] [INFO] Task started: Blastn
[2023-06-18 19:17:51,204] [INFO] Running command: blastn -query GCA_018607185.1_ASM1860718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference/reference_markers.fasta -out GCA_018607185.1_ASM1860718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:51,850] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:51,860] [INFO] Selected 20 target genomes.
[2023-06-18 19:17:51,861] [INFO] Target genome list was writen to GCA_018607185.1_ASM1860718v1_genomic.fna/target_genomes.txt
[2023-06-18 19:17:51,864] [INFO] Task started: fastANI
[2023-06-18 19:17:51,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg715e89f7-3626-4f95-88e1-442b8c256ca0/GCA_018607185.1_ASM1860718v1_genomic.fna.gz --refList GCA_018607185.1_ASM1860718v1_genomic.fna/target_genomes.txt --output GCA_018607185.1_ASM1860718v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:18:03,515] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:03,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:18:03,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:18:03,519] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:18:03,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:18:03,520] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.2051	50	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:18:03,522] [INFO] DFAST Taxonomy check result was written to GCA_018607185.1_ASM1860718v1_genomic.fna/tc_result.tsv
[2023-06-18 19:18:03,522] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:18:03,522] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:18:03,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference/checkm_data
[2023-06-18 19:18:03,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:18:03,553] [INFO] Task started: CheckM
[2023-06-18 19:18:03,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607185.1_ASM1860718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607185.1_ASM1860718v1_genomic.fna/checkm_input GCA_018607185.1_ASM1860718v1_genomic.fna/checkm_result
[2023-06-18 19:18:43,385] [INFO] Task succeeded: CheckM
[2023-06-18 19:18:43,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:18:43,402] [INFO] ===== Completeness check finished =====
[2023-06-18 19:18:43,403] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:18:43,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607185.1_ASM1860718v1_genomic.fna/markers.fasta)
[2023-06-18 19:18:43,404] [INFO] Task started: Blastn
[2023-06-18 19:18:43,404] [INFO] Running command: blastn -query GCA_018607185.1_ASM1860718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab2c122a-a788-422f-b11b-59636b37e1c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607185.1_ASM1860718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:18:44,436] [INFO] Task succeeded: Blastn
[2023-06-18 19:18:44,440] [INFO] Selected 9 target genomes.
[2023-06-18 19:18:44,440] [INFO] Target genome list was writen to GCA_018607185.1_ASM1860718v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:18:44,447] [INFO] Task started: fastANI
[2023-06-18 19:18:44,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg715e89f7-3626-4f95-88e1-442b8c256ca0/GCA_018607185.1_ASM1860718v1_genomic.fna.gz --refList GCA_018607185.1_ASM1860718v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607185.1_ASM1860718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:18:49,216] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:49,233] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:18:49,233] [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_002292345.1	s__BACL24 sp002292345	99.3581	626	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.51	99.36	0.91	0.87	10	conclusive
GCA_017854655.1	s__BACL24 sp017854655	93.278	545	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
GCA_905182435.1	s__BACL24 sp905182435	88.6626	382	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430605.1	s__BACL24 sp002430605	88.2033	524	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.69	99.69	0.90	0.90	2	-
GCA_018663485.1	s__BACL24 sp018663485	86.4977	424	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479975.1	s__BACL24 sp905479975	80.0688	355	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902728235.1	s__BACL24 sp902728235	79.7554	319	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.30	98.39	0.95	0.90	8	-
GCA_018607135.1	s__BACL24 sp003485085	77.7113	104	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
GCA_003331195.1	s__UBA7441 sp003331195	76.6591	57	713	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:18:49,236] [INFO] GTDB search result was written to GCA_018607185.1_ASM1860718v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:18:49,236] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:18:49,241] [INFO] DFAST_QC result json was written to GCA_018607185.1_ASM1860718v1_genomic.fna/dqc_result.json
[2023-06-18 19:18:49,241] [INFO] DFAST_QC completed!
[2023-06-18 19:18:49,241] [INFO] Total running time: 0h1m12s