[2024-01-24 10:47:08,202] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:08,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:08,204] [INFO] DQC Reference Directory: /var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference
[2024-01-24 10:47:11,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,922] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,923] [INFO] Running command: gunzip -c /var/lib/cwl/stg70729d87-c666-4aa6-a76d-caf24ea5c670/GCF_004343345.1_ASM434334v1_genomic.fna.gz | prodigal -d GCF_004343345.1_ASM434334v1_genomic.fna/cds.fna -a GCF_004343345.1_ASM434334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,631] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,632] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,632] [INFO] Running command: hmmsearch --tblout GCF_004343345.1_ASM434334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference/reference_markers.hmm GCF_004343345.1_ASM434334v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,911] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,947] [INFO] Query marker FASTA was written to GCF_004343345.1_ASM434334v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,948] [INFO] Task started: Blastn
[2024-01-24 10:47:23,948] [INFO] Running command: blastn -query GCF_004343345.1_ASM434334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference/reference_markers.fasta -out GCF_004343345.1_ASM434334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:24,548] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:24,553] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:24,554] [INFO] Target genome list was writen to GCF_004343345.1_ASM434334v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,111] [INFO] Task started: fastANI
[2024-01-24 10:47:25,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg70729d87-c666-4aa6-a76d-caf24ea5c670/GCF_004343345.1_ASM434334v1_genomic.fna.gz --refList GCF_004343345.1_ASM434334v1_genomic.fna/target_genomes.txt --output GCF_004343345.1_ASM434334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:35,117] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:35,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:35,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:35,134] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:35,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:35,134] [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
Effusibacillus lacus	strain=DSM 27172	GCA_004343345.1	1348429	1348429	type	True	100.0	1257	1257	95	conclusive
Effusibacillus lacus	strain=skLN1	GCA_002335525.1	1348429	1348429	type	True	99.9911	1253	1257	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 10:47:35,136] [INFO] DFAST Taxonomy check result was written to GCF_004343345.1_ASM434334v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:35,137] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:35,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:35,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference/checkm_data
[2024-01-24 10:47:35,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:35,195] [INFO] Task started: CheckM
[2024-01-24 10:47:35,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004343345.1_ASM434334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004343345.1_ASM434334v1_genomic.fna/checkm_input GCF_004343345.1_ASM434334v1_genomic.fna/checkm_result
[2024-01-24 10:48:13,491] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:13,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:13,517] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:13,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:13,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004343345.1_ASM434334v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:13,518] [INFO] Task started: Blastn
[2024-01-24 10:48:13,519] [INFO] Running command: blastn -query GCF_004343345.1_ASM434334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27b33ea2-eb69-4dd5-b5fe-977b62128910/dqc_reference/reference_markers_gtdb.fasta -out GCF_004343345.1_ASM434334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:14,456] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:14,463] [INFO] Selected 22 target genomes.
[2024-01-24 10:48:14,463] [INFO] Target genome list was writen to GCF_004343345.1_ASM434334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:14,518] [INFO] Task started: fastANI
[2024-01-24 10:48:14,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg70729d87-c666-4aa6-a76d-caf24ea5c670/GCF_004343345.1_ASM434334v1_genomic.fna.gz --refList GCF_004343345.1_ASM434334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004343345.1_ASM434334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:31,075] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:31,080] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:31,080] [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_002335525.1	s__Effusibacillus lacus	99.9911	1253	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tumebacillales;f__Effusibacillaceae;g__Effusibacillus	95.0	99.99	99.99	1.00	1.00	2	conclusive
--------------------------------------------------------------------------------
[2024-01-24 10:48:31,082] [INFO] GTDB search result was written to GCF_004343345.1_ASM434334v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:31,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:31,086] [INFO] DFAST_QC result json was written to GCF_004343345.1_ASM434334v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:31,087] [INFO] DFAST_QC completed!
[2024-01-24 10:48:31,087] [INFO] Total running time: 0h1m23s