[2023-06-04 21:45:29,308] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:45:29,312] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:45:29,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference
[2023-06-04 21:45:30,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:45:30,691] [INFO] Task started: Prodigal
[2023-06-04 21:45:30,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgc054c4d0-5112-4642-9392-8fba835dabc9/GCA_001783045.1_ASM178304v1_genomic.fna.gz | prodigal -d GCA_001783045.1_ASM178304v1_genomic.fna/cds.fna -a GCA_001783045.1_ASM178304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:45:38,364] [INFO] Task succeeded: Prodigal
[2023-06-04 21:45:38,364] [INFO] Task started: HMMsearch
[2023-06-04 21:45:38,365] [INFO] Running command: hmmsearch --tblout GCA_001783045.1_ASM178304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference/reference_markers.hmm GCA_001783045.1_ASM178304v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:45:38,617] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:45:38,619] [INFO] Found 6/6 markers.
[2023-06-04 21:45:38,643] [INFO] Query marker FASTA was written to GCA_001783045.1_ASM178304v1_genomic.fna/markers.fasta
[2023-06-04 21:45:38,644] [INFO] Task started: Blastn
[2023-06-04 21:45:38,644] [INFO] Running command: blastn -query GCA_001783045.1_ASM178304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference/reference_markers.fasta -out GCA_001783045.1_ASM178304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:45:39,290] [INFO] Task succeeded: Blastn
[2023-06-04 21:45:39,294] [INFO] Selected 12 target genomes.
[2023-06-04 21:45:39,295] [INFO] Target genome list was writen to GCA_001783045.1_ASM178304v1_genomic.fna/target_genomes.txt
[2023-06-04 21:45:39,300] [INFO] Task started: fastANI
[2023-06-04 21:45:39,300] [INFO] Running command: fastANI --query /var/lib/cwl/stgc054c4d0-5112-4642-9392-8fba835dabc9/GCA_001783045.1_ASM178304v1_genomic.fna.gz --refList GCA_001783045.1_ASM178304v1_genomic.fna/target_genomes.txt --output GCA_001783045.1_ASM178304v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:45:46,670] [INFO] Task succeeded: fastANI
[2023-06-04 21:45:46,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:45:46,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:45:46,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:45:46,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:45:46,673] [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
--------------------------------------------------------------------------------
[2023-06-04 21:45:46,676] [INFO] DFAST Taxonomy check result was written to GCA_001783045.1_ASM178304v1_genomic.fna/tc_result.tsv
[2023-06-04 21:45:46,677] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:45:46,677] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:45:46,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference/checkm_data
[2023-06-04 21:45:46,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:45:46,697] [INFO] Task started: CheckM
[2023-06-04 21:45:46,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001783045.1_ASM178304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001783045.1_ASM178304v1_genomic.fna/checkm_input GCA_001783045.1_ASM178304v1_genomic.fna/checkm_result
[2023-06-04 21:46:15,077] [INFO] Task succeeded: CheckM
[2023-06-04 21:46:15,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:46:15,099] [INFO] ===== Completeness check finished =====
[2023-06-04 21:46:15,099] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:46:15,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001783045.1_ASM178304v1_genomic.fna/markers.fasta)
[2023-06-04 21:46:15,100] [INFO] Task started: Blastn
[2023-06-04 21:46:15,100] [INFO] Running command: blastn -query GCA_001783045.1_ASM178304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg652d2d1f-7813-4078-b81f-9aa6dd26e2c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_001783045.1_ASM178304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:15,919] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:15,924] [INFO] Selected 17 target genomes.
[2023-06-04 21:46:15,924] [INFO] Target genome list was writen to GCA_001783045.1_ASM178304v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:46:16,036] [INFO] Task started: fastANI
[2023-06-04 21:46:16,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgc054c4d0-5112-4642-9392-8fba835dabc9/GCA_001783045.1_ASM178304v1_genomic.fna.gz --refList GCA_001783045.1_ASM178304v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001783045.1_ASM178304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:46:19,657] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:19,660] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:46:19,660] [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_001784285.1	s__UBA10181 sp001784285	99.9716	354	364	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__UBA10181	95.0	99.97	99.95	0.98	0.97	4	conclusive
--------------------------------------------------------------------------------
[2023-06-04 21:46:19,662] [INFO] GTDB search result was written to GCA_001783045.1_ASM178304v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:46:19,663] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:46:19,665] [INFO] DFAST_QC result json was written to GCA_001783045.1_ASM178304v1_genomic.fna/dqc_result.json
[2023-06-04 21:46:19,665] [INFO] DFAST_QC completed!
[2023-06-04 21:46:19,665] [INFO] Total running time: 0h0m50s