[2024-01-24 13:31:57,535] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:57,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:57,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference
[2024-01-24 13:31:58,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:58,902] [INFO] Task started: Prodigal
[2024-01-24 13:31:58,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg343a472c-a209-4f97-a4ef-38a867c58a97/GCF_014651515.1_ASM1465151v1_genomic.fna.gz | prodigal -d GCF_014651515.1_ASM1465151v1_genomic.fna/cds.fna -a GCF_014651515.1_ASM1465151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:11,001] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:11,002] [INFO] Task started: HMMsearch
[2024-01-24 13:32:11,002] [INFO] Running command: hmmsearch --tblout GCF_014651515.1_ASM1465151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference/reference_markers.hmm GCF_014651515.1_ASM1465151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:11,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:11,242] [INFO] Found 6/6 markers.
[2024-01-24 13:32:11,275] [INFO] Query marker FASTA was written to GCF_014651515.1_ASM1465151v1_genomic.fna/markers.fasta
[2024-01-24 13:32:11,275] [INFO] Task started: Blastn
[2024-01-24 13:32:11,275] [INFO] Running command: blastn -query GCF_014651515.1_ASM1465151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference/reference_markers.fasta -out GCF_014651515.1_ASM1465151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:11,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:11,940] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:11,941] [INFO] Target genome list was writen to GCF_014651515.1_ASM1465151v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:11,950] [INFO] Task started: fastANI
[2024-01-24 13:32:11,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg343a472c-a209-4f97-a4ef-38a867c58a97/GCF_014651515.1_ASM1465151v1_genomic.fna.gz --refList GCF_014651515.1_ASM1465151v1_genomic.fna/target_genomes.txt --output GCF_014651515.1_ASM1465151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:25,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:25,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:25,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:25,434] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:25,434] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:25,434] [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
Arenicella chitinivorans	strain=KCTC 12711	GCA_014651515.1	1329800	1329800	type	True	100.0	1333	1336	95	conclusive
Arenicella xantha	strain=DSM 24032	GCA_003315245.1	644221	644221	type	True	79.3458	187	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:25,436] [INFO] DFAST Taxonomy check result was written to GCF_014651515.1_ASM1465151v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:25,437] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:25,437] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:25,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference/checkm_data
[2024-01-24 13:32:25,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:25,477] [INFO] Task started: CheckM
[2024-01-24 13:32:25,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651515.1_ASM1465151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651515.1_ASM1465151v1_genomic.fna/checkm_input GCF_014651515.1_ASM1465151v1_genomic.fna/checkm_result
[2024-01-24 13:33:04,588] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:04,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:04,607] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:04,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:04,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651515.1_ASM1465151v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:04,608] [INFO] Task started: Blastn
[2024-01-24 13:33:04,608] [INFO] Running command: blastn -query GCF_014651515.1_ASM1465151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5613775a-9f0b-4209-84f4-1841b89c9f4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651515.1_ASM1465151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:05,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:05,716] [INFO] Selected 22 target genomes.
[2024-01-24 13:33:05,716] [INFO] Target genome list was writen to GCF_014651515.1_ASM1465151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:05,794] [INFO] Task started: fastANI
[2024-01-24 13:33:05,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg343a472c-a209-4f97-a4ef-38a867c58a97/GCF_014651515.1_ASM1465151v1_genomic.fna.gz --refList GCF_014651515.1_ASM1465151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651515.1_ASM1465151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:20,413] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,418] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:20,418] [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
GCF_014651515.1	s__Arenicella chitinivorans	100.0	1333	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003315245.1	s__Arenicella xantha	79.3458	187	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002025.1	s__Arenicella sp013002025	77.5146	57	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854775.1	s__Arenicella sp017854775	76.2346	58	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__Arenicellaceae;g__Arenicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,419] [INFO] GTDB search result was written to GCF_014651515.1_ASM1465151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:20,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:20,422] [INFO] DFAST_QC result json was written to GCF_014651515.1_ASM1465151v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:20,422] [INFO] DFAST_QC completed!
[2024-01-24 13:33:20,423] [INFO] Total running time: 0h1m23s