[2023-06-27 18:42:36,692] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:42:36,694] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:42:36,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference
[2023-06-27 18:42:38,002] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:42:38,003] [INFO] Task started: Prodigal
[2023-06-27 18:42:38,003] [INFO] Running command: gunzip -c /var/lib/cwl/stge4ac8624-d1ce-49fe-afea-473a2e6a1b86/GCA_002705145.1_ASM270514v1_genomic.fna.gz | prodigal -d GCA_002705145.1_ASM270514v1_genomic.fna/cds.fna -a GCA_002705145.1_ASM270514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:42:44,913] [INFO] Task succeeded: Prodigal
[2023-06-27 18:42:44,913] [INFO] Task started: HMMsearch
[2023-06-27 18:42:44,913] [INFO] Running command: hmmsearch --tblout GCA_002705145.1_ASM270514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference/reference_markers.hmm GCA_002705145.1_ASM270514v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:42:45,221] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:42:45,222] [INFO] Found 6/6 markers.
[2023-06-27 18:42:45,258] [INFO] Query marker FASTA was written to GCA_002705145.1_ASM270514v1_genomic.fna/markers.fasta
[2023-06-27 18:42:45,259] [INFO] Task started: Blastn
[2023-06-27 18:42:45,259] [INFO] Running command: blastn -query GCA_002705145.1_ASM270514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference/reference_markers.fasta -out GCA_002705145.1_ASM270514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:42:45,899] [INFO] Task succeeded: Blastn
[2023-06-27 18:42:45,904] [INFO] Selected 32 target genomes.
[2023-06-27 18:42:45,904] [INFO] Target genome list was writen to GCA_002705145.1_ASM270514v1_genomic.fna/target_genomes.txt
[2023-06-27 18:42:45,922] [INFO] Task started: fastANI
[2023-06-27 18:42:45,922] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ac8624-d1ce-49fe-afea-473a2e6a1b86/GCA_002705145.1_ASM270514v1_genomic.fna.gz --refList GCA_002705145.1_ASM270514v1_genomic.fna/target_genomes.txt --output GCA_002705145.1_ASM270514v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:43:03,447] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:03,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:43:03,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:43:03,450] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:43:03,450] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 18:43:03,450] [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
--------------------------------------------------------------------------------
[2023-06-27 18:43:03,452] [INFO] DFAST Taxonomy check result was written to GCA_002705145.1_ASM270514v1_genomic.fna/tc_result.tsv
[2023-06-27 18:43:03,453] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:43:03,453] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:43:03,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference/checkm_data
[2023-06-27 18:43:03,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:43:03,502] [INFO] Task started: CheckM
[2023-06-27 18:43:03,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002705145.1_ASM270514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002705145.1_ASM270514v1_genomic.fna/checkm_input GCA_002705145.1_ASM270514v1_genomic.fna/checkm_result
[2023-06-27 18:43:30,598] [INFO] Task succeeded: CheckM
[2023-06-27 18:43:30,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:43:30,681] [INFO] ===== Completeness check finished =====
[2023-06-27 18:43:30,681] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:43:30,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002705145.1_ASM270514v1_genomic.fna/markers.fasta)
[2023-06-27 18:43:30,682] [INFO] Task started: Blastn
[2023-06-27 18:43:30,682] [INFO] Running command: blastn -query GCA_002705145.1_ASM270514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc17338da-d5e9-4d9c-933a-d82b56e0d65f/dqc_reference/reference_markers_gtdb.fasta -out GCA_002705145.1_ASM270514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:43:31,655] [INFO] Task succeeded: Blastn
[2023-06-27 18:43:31,661] [INFO] Selected 27 target genomes.
[2023-06-27 18:43:31,661] [INFO] Target genome list was writen to GCA_002705145.1_ASM270514v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:43:31,676] [INFO] Task started: fastANI
[2023-06-27 18:43:31,676] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ac8624-d1ce-49fe-afea-473a2e6a1b86/GCA_002705145.1_ASM270514v1_genomic.fna.gz --refList GCA_002705145.1_ASM270514v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002705145.1_ASM270514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:43:46,082] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:46,089] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 18:43:46,090] [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_002457215.1	s__UBA9145 sp002457215	98.9946	876	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.99	98.99	0.90	0.90	2	conclusive
GCA_012103535.1	s__UBA9145 sp012103535	77.2054	167	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723195.1	s__UBA9145 sp002723195	77.1179	86	1043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:43:46,092] [INFO] GTDB search result was written to GCA_002705145.1_ASM270514v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:43:46,092] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:43:46,095] [INFO] DFAST_QC result json was written to GCA_002705145.1_ASM270514v1_genomic.fna/dqc_result.json
[2023-06-27 18:43:46,095] [INFO] DFAST_QC completed!
[2023-06-27 18:43:46,095] [INFO] Total running time: 0h1m9s