[2023-06-19 05:51:23,120] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:23,665] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:23,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference
[2023-06-19 05:51:25,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:51:25,079] [INFO] Task started: Prodigal
[2023-06-19 05:51:25,079] [INFO] Running command: gunzip -c /var/lib/cwl/stg867bc333-cdf5-4ac8-90f6-27c95c3daa03/GCA_018672995.1_ASM1867299v1_genomic.fna.gz | prodigal -d GCA_018672995.1_ASM1867299v1_genomic.fna/cds.fna -a GCA_018672995.1_ASM1867299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:51:39,164] [INFO] Task succeeded: Prodigal
[2023-06-19 05:51:39,164] [INFO] Task started: HMMsearch
[2023-06-19 05:51:39,164] [INFO] Running command: hmmsearch --tblout GCA_018672995.1_ASM1867299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference/reference_markers.hmm GCA_018672995.1_ASM1867299v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:51:39,484] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:51:39,486] [INFO] Found 6/6 markers.
[2023-06-19 05:51:39,538] [INFO] Query marker FASTA was written to GCA_018672995.1_ASM1867299v1_genomic.fna/markers.fasta
[2023-06-19 05:51:39,539] [INFO] Task started: Blastn
[2023-06-19 05:51:39,539] [INFO] Running command: blastn -query GCA_018672995.1_ASM1867299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference/reference_markers.fasta -out GCA_018672995.1_ASM1867299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:40,207] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:40,213] [INFO] Selected 36 target genomes.
[2023-06-19 05:51:40,214] [INFO] Target genome list was writen to GCA_018672995.1_ASM1867299v1_genomic.fna/target_genomes.txt
[2023-06-19 05:51:40,217] [INFO] Task started: fastANI
[2023-06-19 05:51:40,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg867bc333-cdf5-4ac8-90f6-27c95c3daa03/GCA_018672995.1_ASM1867299v1_genomic.fna.gz --refList GCA_018672995.1_ASM1867299v1_genomic.fna/target_genomes.txt --output GCA_018672995.1_ASM1867299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:51:59,769] [INFO] Task succeeded: fastANI
[2023-06-19 05:51:59,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:51:59,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:51:59,773] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:51:59,773] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:51:59,773] [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
--------------------------------------------------------------------------------
[2023-06-19 05:51:59,776] [INFO] DFAST Taxonomy check result was written to GCA_018672995.1_ASM1867299v1_genomic.fna/tc_result.tsv
[2023-06-19 05:51:59,777] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:51:59,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:51:59,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference/checkm_data
[2023-06-19 05:51:59,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:51:59,830] [INFO] Task started: CheckM
[2023-06-19 05:51:59,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018672995.1_ASM1867299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018672995.1_ASM1867299v1_genomic.fna/checkm_input GCA_018672995.1_ASM1867299v1_genomic.fna/checkm_result
[2023-06-19 05:52:45,460] [INFO] Task succeeded: CheckM
[2023-06-19 05:52:45,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.13%
Contamintation: 5.90%
Strain heterogeneity: 91.67%
--------------------------------------------------------------------------------
[2023-06-19 05:52:45,508] [INFO] ===== Completeness check finished =====
[2023-06-19 05:52:45,508] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:52:45,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018672995.1_ASM1867299v1_genomic.fna/markers.fasta)
[2023-06-19 05:52:45,509] [INFO] Task started: Blastn
[2023-06-19 05:52:45,509] [INFO] Running command: blastn -query GCA_018672995.1_ASM1867299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d87b23d-4124-4f3d-b2e0-90a3b2ddee54/dqc_reference/reference_markers_gtdb.fasta -out GCA_018672995.1_ASM1867299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:46,355] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:46,360] [INFO] Selected 27 target genomes.
[2023-06-19 05:52:46,360] [INFO] Target genome list was writen to GCA_018672995.1_ASM1867299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:52:46,373] [INFO] Task started: fastANI
[2023-06-19 05:52:46,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg867bc333-cdf5-4ac8-90f6-27c95c3daa03/GCA_018672995.1_ASM1867299v1_genomic.fna.gz --refList GCA_018672995.1_ASM1867299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018672995.1_ASM1867299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:53:03,337] [INFO] Task succeeded: fastANI
[2023-06-19 05:53:03,342] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:53:03,342] [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_018654745.1	s__JABILA01 sp018654745	99.8502	1356	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__JABILA01	95.0	99.91	99.83	0.93	0.89	4	conclusive
GCA_018650465.1	s__JABILA01 sp018650465	83.5078	780	1529	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__JABILA01	95.0	99.90	99.89	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2023-06-19 05:53:03,345] [INFO] GTDB search result was written to GCA_018672995.1_ASM1867299v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:53:03,347] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:53:03,350] [INFO] DFAST_QC result json was written to GCA_018672995.1_ASM1867299v1_genomic.fna/dqc_result.json
[2023-06-19 05:53:03,350] [INFO] DFAST_QC completed!
[2023-06-19 05:53:03,350] [INFO] Total running time: 0h1m40s