[2023-06-30 14:11:40,850] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:11:40,856] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:11:40,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference
[2023-06-30 14:11:42,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:11:42,075] [INFO] Task started: Prodigal
[2023-06-30 14:11:42,075] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5264b3f-ebee-4cd9-8062-cf2176aa122e/GCA_025359305.1_ASM2535930v1_genomic.fna.gz | prodigal -d GCA_025359305.1_ASM2535930v1_genomic.fna/cds.fna -a GCA_025359305.1_ASM2535930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:11:49,076] [INFO] Task succeeded: Prodigal
[2023-06-30 14:11:49,077] [INFO] Task started: HMMsearch
[2023-06-30 14:11:49,077] [INFO] Running command: hmmsearch --tblout GCA_025359305.1_ASM2535930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference/reference_markers.hmm GCA_025359305.1_ASM2535930v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:11:49,322] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:11:49,324] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd5264b3f-ebee-4cd9-8062-cf2176aa122e/GCA_025359305.1_ASM2535930v1_genomic.fna.gz]
[2023-06-30 14:11:49,353] [INFO] Query marker FASTA was written to GCA_025359305.1_ASM2535930v1_genomic.fna/markers.fasta
[2023-06-30 14:11:49,354] [INFO] Task started: Blastn
[2023-06-30 14:11:49,354] [INFO] Running command: blastn -query GCA_025359305.1_ASM2535930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference/reference_markers.fasta -out GCA_025359305.1_ASM2535930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:11:49,928] [INFO] Task succeeded: Blastn
[2023-06-30 14:11:49,933] [INFO] Selected 32 target genomes.
[2023-06-30 14:11:49,934] [INFO] Target genome list was writen to GCA_025359305.1_ASM2535930v1_genomic.fna/target_genomes.txt
[2023-06-30 14:11:49,942] [INFO] Task started: fastANI
[2023-06-30 14:11:49,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5264b3f-ebee-4cd9-8062-cf2176aa122e/GCA_025359305.1_ASM2535930v1_genomic.fna.gz --refList GCA_025359305.1_ASM2535930v1_genomic.fna/target_genomes.txt --output GCA_025359305.1_ASM2535930v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:12:10,886] [INFO] Task succeeded: fastANI
[2023-06-30 14:12:10,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:12:10,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:12:10,889] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:12:10,889] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 14:12:10,889] [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
--------------------------------------------------------------------------------
[2023-06-30 14:12:10,891] [INFO] DFAST Taxonomy check result was written to GCA_025359305.1_ASM2535930v1_genomic.fna/tc_result.tsv
[2023-06-30 14:12:10,892] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:12:10,893] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:12:10,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference/checkm_data
[2023-06-30 14:12:10,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:12:10,927] [INFO] Task started: CheckM
[2023-06-30 14:12:10,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025359305.1_ASM2535930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025359305.1_ASM2535930v1_genomic.fna/checkm_input GCA_025359305.1_ASM2535930v1_genomic.fna/checkm_result
[2023-06-30 14:12:38,328] [INFO] Task succeeded: CheckM
[2023-06-30 14:12:38,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 14:12:38,353] [INFO] ===== Completeness check finished =====
[2023-06-30 14:12:38,353] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:12:38,353] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025359305.1_ASM2535930v1_genomic.fna/markers.fasta)
[2023-06-30 14:12:38,354] [INFO] Task started: Blastn
[2023-06-30 14:12:38,354] [INFO] Running command: blastn -query GCA_025359305.1_ASM2535930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50c0abb6-1fe4-489f-9afd-0e9ca03c738e/dqc_reference/reference_markers_gtdb.fasta -out GCA_025359305.1_ASM2535930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:12:39,133] [INFO] Task succeeded: Blastn
[2023-06-30 14:12:39,138] [INFO] Selected 32 target genomes.
[2023-06-30 14:12:39,138] [INFO] Target genome list was writen to GCA_025359305.1_ASM2535930v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:12:39,160] [INFO] Task started: fastANI
[2023-06-30 14:12:39,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5264b3f-ebee-4cd9-8062-cf2176aa122e/GCA_025359305.1_ASM2535930v1_genomic.fna.gz --refList GCA_025359305.1_ASM2535930v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025359305.1_ASM2535930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:12:55,831] [INFO] Task succeeded: fastANI
[2023-06-30 14:12:55,838] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 14:12:55,838] [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_003151375.1	s__Aestuariivirga sp003151375	76.7652	78	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015714715.1	s__Aestuariivirga litoralis_A	76.471	80	577	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Aestuariivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:12:55,840] [INFO] GTDB search result was written to GCA_025359305.1_ASM2535930v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:12:55,841] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:12:55,843] [INFO] DFAST_QC result json was written to GCA_025359305.1_ASM2535930v1_genomic.fna/dqc_result.json
[2023-06-30 14:12:55,844] [INFO] DFAST_QC completed!
[2023-06-30 14:12:55,844] [INFO] Total running time: 0h1m15s