[2024-01-24 15:10:37,777] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:37,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:37,779] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference
[2024-01-24 15:10:40,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,099] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg82de2518-edc3-4507-a59c-6f3efe93d715/GCF_014651635.1_ASM1465163v1_genomic.fna.gz | prodigal -d GCF_014651635.1_ASM1465163v1_genomic.fna/cds.fna -a GCF_014651635.1_ASM1465163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:04,999] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:05,000] [INFO] Task started: HMMsearch
[2024-01-24 15:11:05,000] [INFO] Running command: hmmsearch --tblout GCF_014651635.1_ASM1465163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference/reference_markers.hmm GCF_014651635.1_ASM1465163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:05,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:05,333] [INFO] Found 6/6 markers.
[2024-01-24 15:11:05,372] [INFO] Query marker FASTA was written to GCF_014651635.1_ASM1465163v1_genomic.fna/markers.fasta
[2024-01-24 15:11:05,373] [INFO] Task started: Blastn
[2024-01-24 15:11:05,373] [INFO] Running command: blastn -query GCF_014651635.1_ASM1465163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference/reference_markers.fasta -out GCF_014651635.1_ASM1465163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:06,041] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:06,046] [INFO] Selected 15 target genomes.
[2024-01-24 15:11:06,046] [INFO] Target genome list was writen to GCF_014651635.1_ASM1465163v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:06,053] [INFO] Task started: fastANI
[2024-01-24 15:11:06,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg82de2518-edc3-4507-a59c-6f3efe93d715/GCF_014651635.1_ASM1465163v1_genomic.fna.gz --refList GCF_014651635.1_ASM1465163v1_genomic.fna/target_genomes.txt --output GCF_014651635.1_ASM1465163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:18,681] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:18,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:18,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:18,687] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:18,687] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:18,687] [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
Cerasicoccus arenae	strain=KCTC 12870	GCA_014651635.1	424488	424488	type	True	100.0	1346	1348	95	conclusive
Cerasicoccus arenae	strain=KCTC 12870	GCA_016595555.1	424488	424488	type	True	99.9716	1295	1348	95	conclusive
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	76.3699	78	1348	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:18,688] [INFO] DFAST Taxonomy check result was written to GCF_014651635.1_ASM1465163v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:18,689] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:18,689] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:18,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference/checkm_data
[2024-01-24 15:11:18,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:18,739] [INFO] Task started: CheckM
[2024-01-24 15:11:18,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651635.1_ASM1465163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651635.1_ASM1465163v1_genomic.fna/checkm_input GCF_014651635.1_ASM1465163v1_genomic.fna/checkm_result
[2024-01-24 15:12:25,226] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:25,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:25,249] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:25,249] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:25,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651635.1_ASM1465163v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:25,250] [INFO] Task started: Blastn
[2024-01-24 15:12:25,251] [INFO] Running command: blastn -query GCF_014651635.1_ASM1465163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84d0a50c-36a1-4cbb-afa7-68e05300562c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651635.1_ASM1465163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:26,124] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:26,129] [INFO] Selected 21 target genomes.
[2024-01-24 15:12:26,130] [INFO] Target genome list was writen to GCF_014651635.1_ASM1465163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:26,148] [INFO] Task started: fastANI
[2024-01-24 15:12:26,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg82de2518-edc3-4507-a59c-6f3efe93d715/GCF_014651635.1_ASM1465163v1_genomic.fna.gz --refList GCF_014651635.1_ASM1465163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651635.1_ASM1465163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:37,860] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:37,867] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:37,867] [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_014651635.1	s__Cerasicoccus arenae	100.0	1346	1348	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__KCTC-12870;g__Cerasicoccus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014230085.1	s__Ruficoccus amylovorans	76.3699	78	1348	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__KCTC-12870;g__Ruficoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:37,869] [INFO] GTDB search result was written to GCF_014651635.1_ASM1465163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:37,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:37,871] [INFO] DFAST_QC result json was written to GCF_014651635.1_ASM1465163v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:37,871] [INFO] DFAST_QC completed!
[2024-01-24 15:12:37,872] [INFO] Total running time: 0h2m0s