[2023-06-19 10:30:23,181] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:30:23,184] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:30:23,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference
[2023-06-19 10:30:24,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:30:24,648] [INFO] Task started: Prodigal
[2023-06-19 10:30:24,648] [INFO] Running command: gunzip -c /var/lib/cwl/stga45369cc-6aed-449f-8a77-eaa993a73bcf/GCA_018673175.1_ASM1867317v1_genomic.fna.gz | prodigal -d GCA_018673175.1_ASM1867317v1_genomic.fna/cds.fna -a GCA_018673175.1_ASM1867317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:30:30,532] [INFO] Task succeeded: Prodigal
[2023-06-19 10:30:30,533] [INFO] Task started: HMMsearch
[2023-06-19 10:30:30,533] [INFO] Running command: hmmsearch --tblout GCA_018673175.1_ASM1867317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference/reference_markers.hmm GCA_018673175.1_ASM1867317v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:30:30,782] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:30:30,784] [INFO] Found 6/6 markers.
[2023-06-19 10:30:30,805] [INFO] Query marker FASTA was written to GCA_018673175.1_ASM1867317v1_genomic.fna/markers.fasta
[2023-06-19 10:30:30,805] [INFO] Task started: Blastn
[2023-06-19 10:30:30,805] [INFO] Running command: blastn -query GCA_018673175.1_ASM1867317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference/reference_markers.fasta -out GCA_018673175.1_ASM1867317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:30:31,423] [INFO] Task succeeded: Blastn
[2023-06-19 10:30:31,427] [INFO] Selected 35 target genomes.
[2023-06-19 10:30:31,427] [INFO] Target genome list was writen to GCA_018673175.1_ASM1867317v1_genomic.fna/target_genomes.txt
[2023-06-19 10:30:31,431] [INFO] Task started: fastANI
[2023-06-19 10:30:31,431] [INFO] Running command: fastANI --query /var/lib/cwl/stga45369cc-6aed-449f-8a77-eaa993a73bcf/GCA_018673175.1_ASM1867317v1_genomic.fna.gz --refList GCA_018673175.1_ASM1867317v1_genomic.fna/target_genomes.txt --output GCA_018673175.1_ASM1867317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:30:56,566] [INFO] Task succeeded: fastANI
[2023-06-19 10:30:56,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:30:56,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:30:56,569] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:30:56,569] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:30:56,569] [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
--------------------------------------------------------------------------------
[2023-06-19 10:30:56,571] [INFO] DFAST Taxonomy check result was written to GCA_018673175.1_ASM1867317v1_genomic.fna/tc_result.tsv
[2023-06-19 10:30:56,571] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:30:56,571] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:30:56,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference/checkm_data
[2023-06-19 10:30:56,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:30:56,595] [INFO] Task started: CheckM
[2023-06-19 10:30:56,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018673175.1_ASM1867317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018673175.1_ASM1867317v1_genomic.fna/checkm_input GCA_018673175.1_ASM1867317v1_genomic.fna/checkm_result
[2023-06-19 10:31:19,422] [INFO] Task succeeded: CheckM
[2023-06-19 10:31:19,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.68%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:31:19,448] [INFO] ===== Completeness check finished =====
[2023-06-19 10:31:19,448] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:31:19,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018673175.1_ASM1867317v1_genomic.fna/markers.fasta)
[2023-06-19 10:31:19,449] [INFO] Task started: Blastn
[2023-06-19 10:31:19,449] [INFO] Running command: blastn -query GCA_018673175.1_ASM1867317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg558e37b4-9958-495a-ab35-45e799a77d96/dqc_reference/reference_markers_gtdb.fasta -out GCA_018673175.1_ASM1867317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:31:20,279] [INFO] Task succeeded: Blastn
[2023-06-19 10:31:20,307] [INFO] Selected 15 target genomes.
[2023-06-19 10:31:20,308] [INFO] Target genome list was writen to GCA_018673175.1_ASM1867317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:31:20,315] [INFO] Task started: fastANI
[2023-06-19 10:31:20,316] [INFO] Running command: fastANI --query /var/lib/cwl/stga45369cc-6aed-449f-8a77-eaa993a73bcf/GCA_018673175.1_ASM1867317v1_genomic.fna.gz --refList GCA_018673175.1_ASM1867317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018673175.1_ASM1867317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:31:27,358] [INFO] Task succeeded: fastANI
[2023-06-19 10:31:27,365] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:31:27,365] [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_018673175.1	s__UBA8337 sp018673175	100.0	569	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018660505.1	s__UBA8337 sp018660505	85.4443	488	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.75	99.71	0.96	0.95	3	-
GCA_900197605.1	s__UBA8337 sp900197605	78.1041	235	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	96.88	95.59	0.86	0.84	6	-
GCA_009920875.1	s__UBA8337 sp009920875	78.0096	174	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	97.55	97.55	0.89	0.89	2	-
GCA_016779015.1	s__UBA8337 sp016779015	77.5866	161	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721725.1	s__UBA8337 sp002721725	77.494	176	575	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__RS24;g__UBA8337	95.0	99.29	99.29	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-19 10:31:27,367] [INFO] GTDB search result was written to GCA_018673175.1_ASM1867317v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:31:27,368] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:31:27,370] [INFO] DFAST_QC result json was written to GCA_018673175.1_ASM1867317v1_genomic.fna/dqc_result.json
[2023-06-19 10:31:27,370] [INFO] DFAST_QC completed!
[2023-06-19 10:31:27,370] [INFO] Total running time: 0h1m4s