[2024-01-24 13:46:40,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,613] [INFO] DQC Reference Directory: /var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference
[2024-01-24 13:46:41,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:41,992] [INFO] Task started: Prodigal
[2024-01-24 13:46:41,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d3025a5-fabd-4239-aea4-06dc91071df1/GCF_019455445.1_ASM1945544v1_genomic.fna.gz | prodigal -d GCF_019455445.1_ASM1945544v1_genomic.fna/cds.fna -a GCF_019455445.1_ASM1945544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:50,325] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:50,326] [INFO] Task started: HMMsearch
[2024-01-24 13:46:50,326] [INFO] Running command: hmmsearch --tblout GCF_019455445.1_ASM1945544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference/reference_markers.hmm GCF_019455445.1_ASM1945544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:50,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:50,600] [INFO] Found 6/6 markers.
[2024-01-24 13:46:50,627] [INFO] Query marker FASTA was written to GCF_019455445.1_ASM1945544v1_genomic.fna/markers.fasta
[2024-01-24 13:46:50,628] [INFO] Task started: Blastn
[2024-01-24 13:46:50,628] [INFO] Running command: blastn -query GCF_019455445.1_ASM1945544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference/reference_markers.fasta -out GCF_019455445.1_ASM1945544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:51,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:51,339] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:51,339] [INFO] Target genome list was writen to GCF_019455445.1_ASM1945544v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:51,350] [INFO] Task started: fastANI
[2024-01-24 13:46:51,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d3025a5-fabd-4239-aea4-06dc91071df1/GCF_019455445.1_ASM1945544v1_genomic.fna.gz --refList GCF_019455445.1_ASM1945544v1_genomic.fna/target_genomes.txt --output GCF_019455445.1_ASM1945544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:04,231] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:04,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:04,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:04,239] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:04,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:04,239] [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
Pseudaquidulcibacter saccharophilus	strain=SZ9	GCA_019455445.1	2831900	2831900	type	True	100.0	941	942	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:47:04,242] [INFO] DFAST Taxonomy check result was written to GCF_019455445.1_ASM1945544v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:04,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:04,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:04,242] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference/checkm_data
[2024-01-24 13:47:04,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:04,272] [INFO] Task started: CheckM
[2024-01-24 13:47:04,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019455445.1_ASM1945544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019455445.1_ASM1945544v1_genomic.fna/checkm_input GCF_019455445.1_ASM1945544v1_genomic.fna/checkm_result
[2024-01-24 13:47:32,996] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:32,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:33,016] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:33,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:33,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019455445.1_ASM1945544v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:33,017] [INFO] Task started: Blastn
[2024-01-24 13:47:33,017] [INFO] Running command: blastn -query GCF_019455445.1_ASM1945544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca00dac-6197-4a25-972a-6f2df03b6250/dqc_reference/reference_markers_gtdb.fasta -out GCF_019455445.1_ASM1945544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:34,078] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:34,081] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:34,081] [INFO] Target genome list was writen to GCF_019455445.1_ASM1945544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:34,103] [INFO] Task started: fastANI
[2024-01-24 13:47:34,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d3025a5-fabd-4239-aea4-06dc91071df1/GCF_019455445.1_ASM1945544v1_genomic.fna.gz --refList GCF_019455445.1_ASM1945544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019455445.1_ASM1945544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:42,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:42,937] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:42,937] [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_002336965.1	s__UBA1942 sp002336965	98.2224	799	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__UBA1942	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002337085.1	s__UBA1942 sp002337085	87.4527	794	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__UBA1942	95.0	99.97	99.97	0.97	0.97	2	-
GCA_009773395.1	s__UBA1942 sp009773395	76.3177	81	942	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__UBA1942	95.0	99.86	99.86	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:42,940] [INFO] GTDB search result was written to GCF_019455445.1_ASM1945544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:42,940] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:42,946] [INFO] DFAST_QC result json was written to GCF_019455445.1_ASM1945544v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:42,947] [INFO] DFAST_QC completed!
[2024-01-24 13:47:42,947] [INFO] Total running time: 0h1m2s