[2024-01-24 12:14:49,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,015] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference
[2024-01-24 12:14:50,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,293] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a87818b-1ce7-4214-8cc9-f08ffb289ecc/GCF_018304665.1_ASM1830466v1_genomic.fna.gz | prodigal -d GCF_018304665.1_ASM1830466v1_genomic.fna/cds.fna -a GCF_018304665.1_ASM1830466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:02,627] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:02,627] [INFO] Task started: HMMsearch
[2024-01-24 12:15:02,627] [INFO] Running command: hmmsearch --tblout GCF_018304665.1_ASM1830466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference/reference_markers.hmm GCF_018304665.1_ASM1830466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:02,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:02,911] [INFO] Found 6/6 markers.
[2024-01-24 12:15:02,955] [INFO] Query marker FASTA was written to GCF_018304665.1_ASM1830466v1_genomic.fna/markers.fasta
[2024-01-24 12:15:02,955] [INFO] Task started: Blastn
[2024-01-24 12:15:02,955] [INFO] Running command: blastn -query GCF_018304665.1_ASM1830466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference/reference_markers.fasta -out GCF_018304665.1_ASM1830466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:03,704] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:03,709] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:03,710] [INFO] Target genome list was writen to GCF_018304665.1_ASM1830466v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:03,738] [INFO] Task started: fastANI
[2024-01-24 12:15:03,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a87818b-1ce7-4214-8cc9-f08ffb289ecc/GCF_018304665.1_ASM1830466v1_genomic.fna.gz --refList GCF_018304665.1_ASM1830466v1_genomic.fna/target_genomes.txt --output GCF_018304665.1_ASM1830466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:14,569] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:14,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:14,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:14,573] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:14,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:14,574] [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
Chloracidobacterium thermophilum	strain=B	GCA_018304665.1	458033	458033	type	True	100.0	1250	1251	95	conclusive
Chloracidobacterium thermophilum	strain=B	GCA_000226295.1	458033	458033	type	True	99.9833	1229	1251	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:15:14,575] [INFO] DFAST Taxonomy check result was written to GCF_018304665.1_ASM1830466v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:14,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:14,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:14,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference/checkm_data
[2024-01-24 12:15:14,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:14,620] [INFO] Task started: CheckM
[2024-01-24 12:15:14,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018304665.1_ASM1830466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018304665.1_ASM1830466v1_genomic.fna/checkm_input GCF_018304665.1_ASM1830466v1_genomic.fna/checkm_result
[2024-01-24 12:15:56,250] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:56,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,276] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:56,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:56,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018304665.1_ASM1830466v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:56,277] [INFO] Task started: Blastn
[2024-01-24 12:15:56,278] [INFO] Running command: blastn -query GCF_018304665.1_ASM1830466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg663d8867-e962-4f38-877f-21b5c529e556/dqc_reference/reference_markers_gtdb.fasta -out GCF_018304665.1_ASM1830466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:57,173] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:57,177] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:57,178] [INFO] Target genome list was writen to GCF_018304665.1_ASM1830466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:57,199] [INFO] Task started: fastANI
[2024-01-24 12:15:57,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a87818b-1ce7-4214-8cc9-f08ffb289ecc/GCF_018304665.1_ASM1830466v1_genomic.fna.gz --refList GCF_018304665.1_ASM1830466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018304665.1_ASM1830466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:08,611] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:08,621] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:08,622] [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_000226295.1	s__Chloracidobacterium thermophilum	99.9833	1229	1251	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Chloracidobacteriales;f__Chloracidobacteriaceae;g__Chloracidobacterium	95.2206	99.33	98.67	0.98	0.97	3	conclusive
GCF_018304765.1	s__Chloracidobacterium aggregatum	95.1826	1156	1251	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Chloracidobacteriales;f__Chloracidobacteriaceae;g__Chloracidobacterium	95.2206	98.46	95.69	0.98	0.95	7	-
GCA_002254845.1	s__Chloracidobacterium sp002254845	78.2531	538	1251	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Chloracidobacteriales;f__Chloracidobacteriaceae;g__Chloracidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018304825.1	s__Chloracidobacterium validum	78.0337	591	1251	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Chloracidobacteriales;f__Chloracidobacteriaceae;g__Chloracidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:08,624] [INFO] GTDB search result was written to GCF_018304665.1_ASM1830466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:08,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:08,627] [INFO] DFAST_QC result json was written to GCF_018304665.1_ASM1830466v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:08,628] [INFO] DFAST_QC completed!
[2024-01-24 12:16:08,628] [INFO] Total running time: 0h1m20s