[2023-06-17 01:29:22,317] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:29:22,319] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:29:22,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference
[2023-06-17 01:29:25,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:29:25,577] [INFO] Task started: Prodigal
[2023-06-17 01:29:25,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d59dc43-42b6-4a22-a95d-7ee3352b3a77/GCA_013215175.1_ASM1321517v1_genomic.fna.gz | prodigal -d GCA_013215175.1_ASM1321517v1_genomic.fna/cds.fna -a GCA_013215175.1_ASM1321517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:29:33,922] [INFO] Task succeeded: Prodigal
[2023-06-17 01:29:33,923] [INFO] Task started: HMMsearch
[2023-06-17 01:29:33,923] [INFO] Running command: hmmsearch --tblout GCA_013215175.1_ASM1321517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference/reference_markers.hmm GCA_013215175.1_ASM1321517v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:29:34,175] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:29:34,176] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2d59dc43-42b6-4a22-a95d-7ee3352b3a77/GCA_013215175.1_ASM1321517v1_genomic.fna.gz]
[2023-06-17 01:29:34,211] [INFO] Query marker FASTA was written to GCA_013215175.1_ASM1321517v1_genomic.fna/markers.fasta
[2023-06-17 01:29:34,212] [INFO] Task started: Blastn
[2023-06-17 01:29:34,212] [INFO] Running command: blastn -query GCA_013215175.1_ASM1321517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference/reference_markers.fasta -out GCA_013215175.1_ASM1321517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:34,889] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:34,893] [INFO] Selected 14 target genomes.
[2023-06-17 01:29:34,894] [INFO] Target genome list was writen to GCA_013215175.1_ASM1321517v1_genomic.fna/target_genomes.txt
[2023-06-17 01:29:34,900] [INFO] Task started: fastANI
[2023-06-17 01:29:34,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d59dc43-42b6-4a22-a95d-7ee3352b3a77/GCA_013215175.1_ASM1321517v1_genomic.fna.gz --refList GCA_013215175.1_ASM1321517v1_genomic.fna/target_genomes.txt --output GCA_013215175.1_ASM1321517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:29:46,250] [INFO] Task succeeded: fastANI
[2023-06-17 01:29:46,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:29:46,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:29:46,260] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:29:46,260] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:29:46,260] [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
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	77.8007	189	853	95	below_threshold
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	77.6856	219	853	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.2472	60	853	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.2115	58	853	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.1786	61	853	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:29:46,264] [INFO] DFAST Taxonomy check result was written to GCA_013215175.1_ASM1321517v1_genomic.fna/tc_result.tsv
[2023-06-17 01:29:46,265] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:29:46,265] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:29:46,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference/checkm_data
[2023-06-17 01:29:46,267] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:29:46,307] [INFO] Task started: CheckM
[2023-06-17 01:29:46,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013215175.1_ASM1321517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013215175.1_ASM1321517v1_genomic.fna/checkm_input GCA_013215175.1_ASM1321517v1_genomic.fna/checkm_result
[2023-06-17 01:30:16,230] [INFO] Task succeeded: CheckM
[2023-06-17 01:30:16,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.37%
Contamintation: 3.24%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2023-06-17 01:30:16,258] [INFO] ===== Completeness check finished =====
[2023-06-17 01:30:16,258] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:30:16,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013215175.1_ASM1321517v1_genomic.fna/markers.fasta)
[2023-06-17 01:30:16,259] [INFO] Task started: Blastn
[2023-06-17 01:30:16,260] [INFO] Running command: blastn -query GCA_013215175.1_ASM1321517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b45733f-ad82-4c0e-8f4b-878c8a1b9129/dqc_reference/reference_markers_gtdb.fasta -out GCA_013215175.1_ASM1321517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:30:17,144] [INFO] Task succeeded: Blastn
[2023-06-17 01:30:17,149] [INFO] Selected 14 target genomes.
[2023-06-17 01:30:17,149] [INFO] Target genome list was writen to GCA_013215175.1_ASM1321517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:30:17,167] [INFO] Task started: fastANI
[2023-06-17 01:30:17,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d59dc43-42b6-4a22-a95d-7ee3352b3a77/GCA_013215175.1_ASM1321517v1_genomic.fna.gz --refList GCA_013215175.1_ASM1321517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013215175.1_ASM1321517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:30:26,568] [INFO] Task succeeded: fastANI
[2023-06-17 01:30:26,578] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:30:26,578] [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_013215175.1	s__Parvularcula sp013215175	100.0	842	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014651915.1	s__Parvularcula lutaonensis	77.8007	189	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085255.1	s__Parvularcula mediterranea	77.7049	217	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	76.1786	61	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001657385.1	s__Marinicaulis sp001657385	75.8226	58	853	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:30:26,580] [INFO] GTDB search result was written to GCA_013215175.1_ASM1321517v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:30:26,581] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:30:26,584] [INFO] DFAST_QC result json was written to GCA_013215175.1_ASM1321517v1_genomic.fna/dqc_result.json
[2023-06-17 01:30:26,584] [INFO] DFAST_QC completed!
[2023-06-17 01:30:26,584] [INFO] Total running time: 0h1m4s