[2024-01-24 13:21:55,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:55,583] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:55,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference
[2024-01-24 13:21:56,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:56,840] [INFO] Task started: Prodigal
[2024-01-24 13:21:56,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg99f03bc2-e277-43b6-8b17-b7b592ea4a8d/GCF_004115085.1_ASM411508v1_genomic.fna.gz | prodigal -d GCF_004115085.1_ASM411508v1_genomic.fna/cds.fna -a GCF_004115085.1_ASM411508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:05,419] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:05,420] [INFO] Task started: HMMsearch
[2024-01-24 13:22:05,420] [INFO] Running command: hmmsearch --tblout GCF_004115085.1_ASM411508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference/reference_markers.hmm GCF_004115085.1_ASM411508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:05,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:05,726] [INFO] Found 6/6 markers.
[2024-01-24 13:22:05,759] [INFO] Query marker FASTA was written to GCF_004115085.1_ASM411508v1_genomic.fna/markers.fasta
[2024-01-24 13:22:05,760] [INFO] Task started: Blastn
[2024-01-24 13:22:05,760] [INFO] Running command: blastn -query GCF_004115085.1_ASM411508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference/reference_markers.fasta -out GCF_004115085.1_ASM411508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:06,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:06,389] [INFO] Selected 29 target genomes.
[2024-01-24 13:22:06,389] [INFO] Target genome list was writen to GCF_004115085.1_ASM411508v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:06,414] [INFO] Task started: fastANI
[2024-01-24 13:22:06,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg99f03bc2-e277-43b6-8b17-b7b592ea4a8d/GCF_004115085.1_ASM411508v1_genomic.fna.gz --refList GCF_004115085.1_ASM411508v1_genomic.fna/target_genomes.txt --output GCF_004115085.1_ASM411508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:25,991] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:25,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:25,992] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:25,995] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:25,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:25,996] [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
Longirhabdus pacifica	strain=SCSIO 06110	GCA_004115085.1	2305227	2305227	type	True	100.0	1220	1225	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,997] [INFO] DFAST Taxonomy check result was written to GCF_004115085.1_ASM411508v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:25,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:25,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:25,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference/checkm_data
[2024-01-24 13:22:25,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:26,042] [INFO] Task started: CheckM
[2024-01-24 13:22:26,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004115085.1_ASM411508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004115085.1_ASM411508v1_genomic.fna/checkm_input GCF_004115085.1_ASM411508v1_genomic.fna/checkm_result
[2024-01-24 13:22:57,320] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:57,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:57,344] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:57,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:57,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004115085.1_ASM411508v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:57,346] [INFO] Task started: Blastn
[2024-01-24 13:22:57,346] [INFO] Running command: blastn -query GCF_004115085.1_ASM411508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg174bf904-6677-4afe-a06c-d2d0f2b38295/dqc_reference/reference_markers_gtdb.fasta -out GCF_004115085.1_ASM411508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:58,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:58,066] [INFO] Selected 28 target genomes.
[2024-01-24 13:22:58,066] [INFO] Target genome list was writen to GCF_004115085.1_ASM411508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:58,157] [INFO] Task started: fastANI
[2024-01-24 13:22:58,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg99f03bc2-e277-43b6-8b17-b7b592ea4a8d/GCF_004115085.1_ASM411508v1_genomic.fna.gz --refList GCF_004115085.1_ASM411508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004115085.1_ASM411508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:16,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:16,045] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:16,045] [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_004115085.1	s__Longirhabdus pacifica	100.0	1220	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__SCSIO-06110;g__Longirhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:23:16,047] [INFO] GTDB search result was written to GCF_004115085.1_ASM411508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:16,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:16,050] [INFO] DFAST_QC result json was written to GCF_004115085.1_ASM411508v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:16,050] [INFO] DFAST_QC completed!
[2024-01-24 13:23:16,050] [INFO] Total running time: 0h1m20s