[2023-06-18 22:56:40,756] [INFO] DFAST_QC pipeline started.
[2023-06-18 22:56:40,758] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 22:56:40,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference
[2023-06-18 22:56:42,003] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 22:56:42,004] [INFO] Task started: Prodigal
[2023-06-18 22:56:42,004] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ef28ec1-291b-4c58-9949-9564538da884/GCA_018656975.1_ASM1865697v1_genomic.fna.gz | prodigal -d GCA_018656975.1_ASM1865697v1_genomic.fna/cds.fna -a GCA_018656975.1_ASM1865697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 22:56:52,828] [INFO] Task succeeded: Prodigal
[2023-06-18 22:56:52,829] [INFO] Task started: HMMsearch
[2023-06-18 22:56:52,829] [INFO] Running command: hmmsearch --tblout GCA_018656975.1_ASM1865697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference/reference_markers.hmm GCA_018656975.1_ASM1865697v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 22:56:53,097] [INFO] Task succeeded: HMMsearch
[2023-06-18 22:56:53,099] [INFO] Found 6/6 markers.
[2023-06-18 22:56:53,130] [INFO] Query marker FASTA was written to GCA_018656975.1_ASM1865697v1_genomic.fna/markers.fasta
[2023-06-18 22:56:53,131] [INFO] Task started: Blastn
[2023-06-18 22:56:53,131] [INFO] Running command: blastn -query GCA_018656975.1_ASM1865697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference/reference_markers.fasta -out GCA_018656975.1_ASM1865697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:56:53,817] [INFO] Task succeeded: Blastn
[2023-06-18 22:56:53,820] [INFO] Selected 33 target genomes.
[2023-06-18 22:56:53,821] [INFO] Target genome list was writen to GCA_018656975.1_ASM1865697v1_genomic.fna/target_genomes.txt
[2023-06-18 22:56:53,822] [INFO] Task started: fastANI
[2023-06-18 22:56:53,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef28ec1-291b-4c58-9949-9564538da884/GCA_018656975.1_ASM1865697v1_genomic.fna.gz --refList GCA_018656975.1_ASM1865697v1_genomic.fna/target_genomes.txt --output GCA_018656975.1_ASM1865697v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 22:57:14,513] [INFO] Task succeeded: fastANI
[2023-06-18 22:57:14,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 22:57:14,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 22:57:14,516] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 22:57:14,517] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 22:57:14,517] [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
--------------------------------------------------------------------------------
[2023-06-18 22:57:14,519] [INFO] DFAST Taxonomy check result was written to GCA_018656975.1_ASM1865697v1_genomic.fna/tc_result.tsv
[2023-06-18 22:57:14,519] [INFO] ===== Taxonomy check completed =====
[2023-06-18 22:57:14,520] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 22:57:14,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference/checkm_data
[2023-06-18 22:57:14,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 22:57:14,574] [INFO] Task started: CheckM
[2023-06-18 22:57:14,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018656975.1_ASM1865697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018656975.1_ASM1865697v1_genomic.fna/checkm_input GCA_018656975.1_ASM1865697v1_genomic.fna/checkm_result
[2023-06-18 22:57:50,629] [INFO] Task succeeded: CheckM
[2023-06-18 22:57:50,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 22:57:50,658] [INFO] ===== Completeness check finished =====
[2023-06-18 22:57:50,659] [INFO] ===== Start GTDB Search =====
[2023-06-18 22:57:50,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018656975.1_ASM1865697v1_genomic.fna/markers.fasta)
[2023-06-18 22:57:50,659] [INFO] Task started: Blastn
[2023-06-18 22:57:50,660] [INFO] Running command: blastn -query GCA_018656975.1_ASM1865697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1525c896-15cb-43a0-9813-c494e912b316/dqc_reference/reference_markers_gtdb.fasta -out GCA_018656975.1_ASM1865697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 22:57:51,764] [INFO] Task succeeded: Blastn
[2023-06-18 22:57:51,769] [INFO] Selected 28 target genomes.
[2023-06-18 22:57:51,769] [INFO] Target genome list was writen to GCA_018656975.1_ASM1865697v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 22:57:51,777] [INFO] Task started: fastANI
[2023-06-18 22:57:51,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ef28ec1-291b-4c58-9949-9564538da884/GCA_018656975.1_ASM1865697v1_genomic.fna.gz --refList GCA_018656975.1_ASM1865697v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018656975.1_ASM1865697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 22:58:07,231] [INFO] Task succeeded: fastANI
[2023-06-18 22:58:07,238] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 22:58:07,238] [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_018662225.1	s__JABJGO01 sp018662225	99.916	1043	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JABJGO01	95.0	99.91	99.87	0.94	0.92	10	conclusive
GCA_018664265.1	s__JABJOR01 sp018664265	76.4444	65	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JABJOR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 22:58:07,240] [INFO] GTDB search result was written to GCA_018656975.1_ASM1865697v1_genomic.fna/result_gtdb.tsv
[2023-06-18 22:58:07,241] [INFO] ===== GTDB Search completed =====
[2023-06-18 22:58:07,243] [INFO] DFAST_QC result json was written to GCA_018656975.1_ASM1865697v1_genomic.fna/dqc_result.json
[2023-06-18 22:58:07,243] [INFO] DFAST_QC completed!
[2023-06-18 22:58:07,243] [INFO] Total running time: 0h1m26s