[2023-06-19 13:54:07,124] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:07,126] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:07,126] [INFO] DQC Reference Directory: /var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference
[2023-06-19 13:54:10,066] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:10,068] [INFO] Task started: Prodigal
[2023-06-19 13:54:10,068] [INFO] Running command: gunzip -c /var/lib/cwl/stg150d6892-d535-4e14-968e-07aa7a467cee/GCA_018659125.1_ASM1865912v1_genomic.fna.gz | prodigal -d GCA_018659125.1_ASM1865912v1_genomic.fna/cds.fna -a GCA_018659125.1_ASM1865912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:16,710] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:16,710] [INFO] Task started: HMMsearch
[2023-06-19 13:54:16,711] [INFO] Running command: hmmsearch --tblout GCA_018659125.1_ASM1865912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference/reference_markers.hmm GCA_018659125.1_ASM1865912v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:16,964] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:16,965] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg150d6892-d535-4e14-968e-07aa7a467cee/GCA_018659125.1_ASM1865912v1_genomic.fna.gz]
[2023-06-19 13:54:16,998] [INFO] Query marker FASTA was written to GCA_018659125.1_ASM1865912v1_genomic.fna/markers.fasta
[2023-06-19 13:54:16,998] [INFO] Task started: Blastn
[2023-06-19 13:54:16,998] [INFO] Running command: blastn -query GCA_018659125.1_ASM1865912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference/reference_markers.fasta -out GCA_018659125.1_ASM1865912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:17,627] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:17,631] [INFO] Selected 27 target genomes.
[2023-06-19 13:54:17,631] [INFO] Target genome list was writen to GCA_018659125.1_ASM1865912v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:17,637] [INFO] Task started: fastANI
[2023-06-19 13:54:17,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg150d6892-d535-4e14-968e-07aa7a467cee/GCA_018659125.1_ASM1865912v1_genomic.fna.gz --refList GCA_018659125.1_ASM1865912v1_genomic.fna/target_genomes.txt --output GCA_018659125.1_ASM1865912v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:33,456] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:33,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:33,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:33,463] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:54:33,464] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:54:33,464] [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
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	75.566	51	670	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:54:33,466] [INFO] DFAST Taxonomy check result was written to GCA_018659125.1_ASM1865912v1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:33,467] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:33,468] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:33,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference/checkm_data
[2023-06-19 13:54:33,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:33,505] [INFO] Task started: CheckM
[2023-06-19 13:54:33,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018659125.1_ASM1865912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018659125.1_ASM1865912v1_genomic.fna/checkm_input GCA_018659125.1_ASM1865912v1_genomic.fna/checkm_result
[2023-06-19 13:54:59,671] [INFO] Task succeeded: CheckM
[2023-06-19 13:54:59,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:54:59,695] [INFO] ===== Completeness check finished =====
[2023-06-19 13:54:59,695] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:54:59,695] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018659125.1_ASM1865912v1_genomic.fna/markers.fasta)
[2023-06-19 13:54:59,696] [INFO] Task started: Blastn
[2023-06-19 13:54:59,696] [INFO] Running command: blastn -query GCA_018659125.1_ASM1865912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg013d5d20-b54f-4f96-8027-3e9c91889753/dqc_reference/reference_markers_gtdb.fasta -out GCA_018659125.1_ASM1865912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:55:00,636] [INFO] Task succeeded: Blastn
[2023-06-19 13:55:00,651] [INFO] Selected 21 target genomes.
[2023-06-19 13:55:00,651] [INFO] Target genome list was writen to GCA_018659125.1_ASM1865912v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:55:00,662] [INFO] Task started: fastANI
[2023-06-19 13:55:00,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg150d6892-d535-4e14-968e-07aa7a467cee/GCA_018659125.1_ASM1865912v1_genomic.fna.gz --refList GCA_018659125.1_ASM1865912v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018659125.1_ASM1865912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:55:13,544] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:13,553] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:55:13,553] [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_001642945.1	s__LGRT01 sp001642945	99.2839	651	670	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	conclusive
GCA_016778765.1	s__LGRT01 sp016778765	93.7127	583	670	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	98.26	96.00	0.81	0.61	8	-
GCA_002726375.1	s__CABZJG01 sp002726375	76.2723	52	670	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	-
--------------------------------------------------------------------------------
[2023-06-19 13:55:13,556] [INFO] GTDB search result was written to GCA_018659125.1_ASM1865912v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:55:13,556] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:55:13,559] [INFO] DFAST_QC result json was written to GCA_018659125.1_ASM1865912v1_genomic.fna/dqc_result.json
[2023-06-19 13:55:13,559] [INFO] DFAST_QC completed!
[2023-06-19 13:55:13,559] [INFO] Total running time: 0h1m6s