[2024-01-24 10:47:24,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference
[2024-01-24 10:47:26,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,575] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a451c83-78f3-4050-94a8-1ad264f930d5/GCF_014384785.1_ASM1438478v1_genomic.fna.gz | prodigal -d GCF_014384785.1_ASM1438478v1_genomic.fna/cds.fna -a GCF_014384785.1_ASM1438478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:33,859] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:33,860] [INFO] Task started: HMMsearch
[2024-01-24 10:47:33,860] [INFO] Running command: hmmsearch --tblout GCF_014384785.1_ASM1438478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference/reference_markers.hmm GCF_014384785.1_ASM1438478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:34,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:34,128] [INFO] Found 6/6 markers.
[2024-01-24 10:47:34,154] [INFO] Query marker FASTA was written to GCF_014384785.1_ASM1438478v1_genomic.fna/markers.fasta
[2024-01-24 10:47:34,154] [INFO] Task started: Blastn
[2024-01-24 10:47:34,154] [INFO] Running command: blastn -query GCF_014384785.1_ASM1438478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference/reference_markers.fasta -out GCF_014384785.1_ASM1438478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:34,789] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:34,792] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:34,792] [INFO] Target genome list was writen to GCF_014384785.1_ASM1438478v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:34,809] [INFO] Task started: fastANI
[2024-01-24 10:47:34,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a451c83-78f3-4050-94a8-1ad264f930d5/GCF_014384785.1_ASM1438478v1_genomic.fna.gz --refList GCF_014384785.1_ASM1438478v1_genomic.fna/target_genomes.txt --output GCF_014384785.1_ASM1438478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:43,327] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:43,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:43,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:43,331] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:43,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:43,332] [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
Congzhengia minquanensis	strain=H8	GCA_014384785.1	2763657	2763657	type	True	100.0	925	925	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 10:47:43,333] [INFO] DFAST Taxonomy check result was written to GCF_014384785.1_ASM1438478v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:43,334] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:43,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:43,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference/checkm_data
[2024-01-24 10:47:43,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:43,367] [INFO] Task started: CheckM
[2024-01-24 10:47:43,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384785.1_ASM1438478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384785.1_ASM1438478v1_genomic.fna/checkm_input GCF_014384785.1_ASM1438478v1_genomic.fna/checkm_result
[2024-01-24 10:48:10,536] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:10,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:10,558] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:10,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:10,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384785.1_ASM1438478v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:10,559] [INFO] Task started: Blastn
[2024-01-24 10:48:10,559] [INFO] Running command: blastn -query GCF_014384785.1_ASM1438478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b47cec6-a79d-4d9c-9065-13bdac35e330/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384785.1_ASM1438478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:11,668] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:11,673] [INFO] Selected 27 target genomes.
[2024-01-24 10:48:11,673] [INFO] Target genome list was writen to GCF_014384785.1_ASM1438478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:11,714] [INFO] Task started: fastANI
[2024-01-24 10:48:11,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a451c83-78f3-4050-94a8-1ad264f930d5/GCF_014384785.1_ASM1438478v1_genomic.fna.gz --refList GCF_014384785.1_ASM1438478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384785.1_ASM1438478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:22,575] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:22,582] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:22,583] [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
GCA_014384785.1	s__UBA9506 sp003506415	100.0	925	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UBA9506	95.0	98.09	98.06	0.87	0.82	6	conclusive
GCA_017396465.1	s__UBA9506 sp017396465	76.4682	86	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA9506;g__UBA9506	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:22,585] [INFO] GTDB search result was written to GCF_014384785.1_ASM1438478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:22,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:22,588] [INFO] DFAST_QC result json was written to GCF_014384785.1_ASM1438478v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:22,588] [INFO] DFAST_QC completed!
[2024-01-24 10:48:22,588] [INFO] Total running time: 0h0m58s