[2023-06-18 18:53:18,104] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:53:18,108] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:53:18,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference
[2023-06-18 18:53:19,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:53:19,563] [INFO] Task started: Prodigal
[2023-06-18 18:53:19,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg78de1bd7-2bca-4fef-a682-18d817700ece/GCA_018607165.1_ASM1860716v1_genomic.fna.gz | prodigal -d GCA_018607165.1_ASM1860716v1_genomic.fna/cds.fna -a GCA_018607165.1_ASM1860716v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:53:27,818] [INFO] Task succeeded: Prodigal
[2023-06-18 18:53:27,818] [INFO] Task started: HMMsearch
[2023-06-18 18:53:27,818] [INFO] Running command: hmmsearch --tblout GCA_018607165.1_ASM1860716v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference/reference_markers.hmm GCA_018607165.1_ASM1860716v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:53:28,025] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:53:28,026] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg78de1bd7-2bca-4fef-a682-18d817700ece/GCA_018607165.1_ASM1860716v1_genomic.fna.gz]
[2023-06-18 18:53:28,051] [INFO] Query marker FASTA was written to GCA_018607165.1_ASM1860716v1_genomic.fna/markers.fasta
[2023-06-18 18:53:28,054] [INFO] Task started: Blastn
[2023-06-18 18:53:28,054] [INFO] Running command: blastn -query GCA_018607165.1_ASM1860716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference/reference_markers.fasta -out GCA_018607165.1_ASM1860716v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:53:28,675] [INFO] Task succeeded: Blastn
[2023-06-18 18:53:28,679] [INFO] Selected 11 target genomes.
[2023-06-18 18:53:28,679] [INFO] Target genome list was writen to GCA_018607165.1_ASM1860716v1_genomic.fna/target_genomes.txt
[2023-06-18 18:53:28,681] [INFO] Task started: fastANI
[2023-06-18 18:53:28,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg78de1bd7-2bca-4fef-a682-18d817700ece/GCA_018607165.1_ASM1860716v1_genomic.fna.gz --refList GCA_018607165.1_ASM1860716v1_genomic.fna/target_genomes.txt --output GCA_018607165.1_ASM1860716v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:53:36,606] [INFO] Task succeeded: fastANI
[2023-06-18 18:53:36,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:53:36,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:53:36,610] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:53:36,611] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:53:36,611] [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	76.9693	63	407	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:53:36,614] [INFO] DFAST Taxonomy check result was written to GCA_018607165.1_ASM1860716v1_genomic.fna/tc_result.tsv
[2023-06-18 18:53:36,615] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:53:36,615] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:53:36,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference/checkm_data
[2023-06-18 18:53:36,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:53:36,645] [INFO] Task started: CheckM
[2023-06-18 18:53:36,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607165.1_ASM1860716v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607165.1_ASM1860716v1_genomic.fna/checkm_input GCA_018607165.1_ASM1860716v1_genomic.fna/checkm_result
[2023-06-18 18:54:05,777] [INFO] Task succeeded: CheckM
[2023-06-18 18:54:05,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:54:05,809] [INFO] ===== Completeness check finished =====
[2023-06-18 18:54:05,810] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:54:05,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607165.1_ASM1860716v1_genomic.fna/markers.fasta)
[2023-06-18 18:54:05,811] [INFO] Task started: Blastn
[2023-06-18 18:54:05,811] [INFO] Running command: blastn -query GCA_018607165.1_ASM1860716v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ee54494-5c3b-442b-b861-8b4c7167aebd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607165.1_ASM1860716v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:54:06,636] [INFO] Task succeeded: Blastn
[2023-06-18 18:54:06,641] [INFO] Selected 17 target genomes.
[2023-06-18 18:54:06,641] [INFO] Target genome list was writen to GCA_018607165.1_ASM1860716v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:54:06,645] [INFO] Task started: fastANI
[2023-06-18 18:54:06,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg78de1bd7-2bca-4fef-a682-18d817700ece/GCA_018607165.1_ASM1860716v1_genomic.fna.gz --refList GCA_018607165.1_ASM1860716v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607165.1_ASM1860716v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:54:14,837] [INFO] Task succeeded: fastANI
[2023-06-18 18:54:14,849] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:54:14,849] [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_002480015.1	s__UBA7441 sp002480015	99.5018	332	407	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.46	97.23	0.80	0.69	7	conclusive
GCA_905479975.1	s__BACL24 sp905479975	77.623	60	407	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_002729725.1	s__UBA7441 sp002729725	77.3804	112	407	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
GCF_902728235.1	s__BACL24 sp902728235	77.3729	58	407	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_007692545.1	s__UBA7441 sp007692545	76.8578	71	407	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430605.1	s__BACL24 sp002430605	76.6831	58	407	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_009908325.1	s__UBA7441 sp009908325	76.5211	74	407	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854655.1	s__BACL24 sp017854655	76.3189	53	407	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.39	99.26	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-18 18:54:14,851] [INFO] GTDB search result was written to GCA_018607165.1_ASM1860716v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:54:14,852] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:54:14,855] [INFO] DFAST_QC result json was written to GCA_018607165.1_ASM1860716v1_genomic.fna/dqc_result.json
[2023-06-18 18:54:14,855] [INFO] DFAST_QC completed!
[2023-06-18 18:54:14,855] [INFO] Total running time: 0h0m57s