[2023-06-29 14:39:48,530] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:39:48,533] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:39:48,533] [INFO] DQC Reference Directory: /var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference
[2023-06-29 14:39:49,764] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:39:49,765] [INFO] Task started: Prodigal
[2023-06-29 14:39:49,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f01961d-3995-42c2-b5f9-405a290100cd/GCA_011682565.1_ASM1168256v1_genomic.fna.gz | prodigal -d GCA_011682565.1_ASM1168256v1_genomic.fna/cds.fna -a GCA_011682565.1_ASM1168256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:39:58,978] [INFO] Task succeeded: Prodigal
[2023-06-29 14:39:58,979] [INFO] Task started: HMMsearch
[2023-06-29 14:39:58,979] [INFO] Running command: hmmsearch --tblout GCA_011682565.1_ASM1168256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference/reference_markers.hmm GCA_011682565.1_ASM1168256v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:39:59,246] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:39:59,247] [INFO] Found 6/6 markers.
[2023-06-29 14:39:59,281] [INFO] Query marker FASTA was written to GCA_011682565.1_ASM1168256v1_genomic.fna/markers.fasta
[2023-06-29 14:39:59,281] [INFO] Task started: Blastn
[2023-06-29 14:39:59,281] [INFO] Running command: blastn -query GCA_011682565.1_ASM1168256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference/reference_markers.fasta -out GCA_011682565.1_ASM1168256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:39:59,856] [INFO] Task succeeded: Blastn
[2023-06-29 14:39:59,860] [INFO] Selected 17 target genomes.
[2023-06-29 14:39:59,860] [INFO] Target genome list was writen to GCA_011682565.1_ASM1168256v1_genomic.fna/target_genomes.txt
[2023-06-29 14:39:59,865] [INFO] Task started: fastANI
[2023-06-29 14:39:59,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f01961d-3995-42c2-b5f9-405a290100cd/GCA_011682565.1_ASM1168256v1_genomic.fna.gz --refList GCA_011682565.1_ASM1168256v1_genomic.fna/target_genomes.txt --output GCA_011682565.1_ASM1168256v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:40:13,922] [INFO] Task succeeded: fastANI
[2023-06-29 14:40:13,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:40:13,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:40:13,924] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:40:13,924] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:40:13,924] [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
--------------------------------------------------------------------------------
[2023-06-29 14:40:13,926] [INFO] DFAST Taxonomy check result was written to GCA_011682565.1_ASM1168256v1_genomic.fna/tc_result.tsv
[2023-06-29 14:40:13,927] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:40:13,927] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:40:13,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference/checkm_data
[2023-06-29 14:40:13,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:40:13,971] [INFO] Task started: CheckM
[2023-06-29 14:40:13,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011682565.1_ASM1168256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011682565.1_ASM1168256v1_genomic.fna/checkm_input GCA_011682565.1_ASM1168256v1_genomic.fna/checkm_result
[2023-06-29 14:40:45,649] [INFO] Task succeeded: CheckM
[2023-06-29 14:40:45,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:40:45,669] [INFO] ===== Completeness check finished =====
[2023-06-29 14:40:45,669] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:40:45,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011682565.1_ASM1168256v1_genomic.fna/markers.fasta)
[2023-06-29 14:40:45,669] [INFO] Task started: Blastn
[2023-06-29 14:40:45,669] [INFO] Running command: blastn -query GCA_011682565.1_ASM1168256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc51fa035-7566-4c47-9823-ad23776c2ef9/dqc_reference/reference_markers_gtdb.fasta -out GCA_011682565.1_ASM1168256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:40:46,474] [INFO] Task succeeded: Blastn
[2023-06-29 14:40:46,478] [INFO] Selected 17 target genomes.
[2023-06-29 14:40:46,478] [INFO] Target genome list was writen to GCA_011682565.1_ASM1168256v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:40:46,504] [INFO] Task started: fastANI
[2023-06-29 14:40:46,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f01961d-3995-42c2-b5f9-405a290100cd/GCA_011682565.1_ASM1168256v1_genomic.fna.gz --refList GCA_011682565.1_ASM1168256v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011682565.1_ASM1168256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:40:57,074] [INFO] Task succeeded: fastANI
[2023-06-29 14:40:57,078] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:40:57,078] [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_011682565.1	s__JAADGR01 sp011682565	100.0	1076	1100	d__Bacteria;p__KSB1;c__UBA2214;o__UBA2214;f__Zgenome-0027;g__JAADGR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013152225.1	s__JAADGR01 sp013152225	92.0013	762	1100	d__Bacteria;p__KSB1;c__UBA2214;o__UBA2214;f__Zgenome-0027;g__JAADGR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:40:57,080] [INFO] GTDB search result was written to GCA_011682565.1_ASM1168256v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:40:57,081] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:40:57,083] [INFO] DFAST_QC result json was written to GCA_011682565.1_ASM1168256v1_genomic.fna/dqc_result.json
[2023-06-29 14:40:57,083] [INFO] DFAST_QC completed!
[2023-06-29 14:40:57,083] [INFO] Total running time: 0h1m9s