[2023-06-29 19:34:24,531] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:34:24,535] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:34:24,535] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference
[2023-06-29 19:34:25,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:34:25,947] [INFO] Task started: Prodigal
[2023-06-29 19:34:25,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d7dd77-f3f5-4234-b381-10a56e3fe66c/GCA_011321845.1_ASM1132184v1_genomic.fna.gz | prodigal -d GCA_011321845.1_ASM1132184v1_genomic.fna/cds.fna -a GCA_011321845.1_ASM1132184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:34:36,996] [INFO] Task succeeded: Prodigal
[2023-06-29 19:34:36,997] [INFO] Task started: HMMsearch
[2023-06-29 19:34:36,997] [INFO] Running command: hmmsearch --tblout GCA_011321845.1_ASM1132184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference/reference_markers.hmm GCA_011321845.1_ASM1132184v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:34:37,322] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:34:37,327] [INFO] Found 6/6 markers.
[2023-06-29 19:34:37,366] [INFO] Query marker FASTA was written to GCA_011321845.1_ASM1132184v1_genomic.fna/markers.fasta
[2023-06-29 19:34:37,366] [INFO] Task started: Blastn
[2023-06-29 19:34:37,366] [INFO] Running command: blastn -query GCA_011321845.1_ASM1132184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference/reference_markers.fasta -out GCA_011321845.1_ASM1132184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:34:38,037] [INFO] Task succeeded: Blastn
[2023-06-29 19:34:38,062] [INFO] Selected 18 target genomes.
[2023-06-29 19:34:38,062] [INFO] Target genome list was writen to GCA_011321845.1_ASM1132184v1_genomic.fna/target_genomes.txt
[2023-06-29 19:34:38,096] [INFO] Task started: fastANI
[2023-06-29 19:34:38,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d7dd77-f3f5-4234-b381-10a56e3fe66c/GCA_011321845.1_ASM1132184v1_genomic.fna.gz --refList GCA_011321845.1_ASM1132184v1_genomic.fna/target_genomes.txt --output GCA_011321845.1_ASM1132184v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:34:50,536] [INFO] Task succeeded: fastANI
[2023-06-29 19:34:50,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:34:50,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:34:50,539] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:34:50,539] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:34:50,539] [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 19:34:50,541] [INFO] DFAST Taxonomy check result was written to GCA_011321845.1_ASM1132184v1_genomic.fna/tc_result.tsv
[2023-06-29 19:34:50,542] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:34:50,542] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:34:50,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference/checkm_data
[2023-06-29 19:34:50,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:34:50,591] [INFO] Task started: CheckM
[2023-06-29 19:34:50,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011321845.1_ASM1132184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011321845.1_ASM1132184v1_genomic.fna/checkm_input GCA_011321845.1_ASM1132184v1_genomic.fna/checkm_result
[2023-06-29 19:35:25,706] [INFO] Task succeeded: CheckM
[2023-06-29 19:35:25,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 19:35:25,732] [INFO] ===== Completeness check finished =====
[2023-06-29 19:35:25,732] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:35:25,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011321845.1_ASM1132184v1_genomic.fna/markers.fasta)
[2023-06-29 19:35:25,733] [INFO] Task started: Blastn
[2023-06-29 19:35:25,733] [INFO] Running command: blastn -query GCA_011321845.1_ASM1132184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd9d3fee-cd18-452b-96a0-2fc381c81a01/dqc_reference/reference_markers_gtdb.fasta -out GCA_011321845.1_ASM1132184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:35:26,577] [INFO] Task succeeded: Blastn
[2023-06-29 19:35:26,582] [INFO] Selected 21 target genomes.
[2023-06-29 19:35:26,582] [INFO] Target genome list was writen to GCA_011321845.1_ASM1132184v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:35:26,623] [INFO] Task started: fastANI
[2023-06-29 19:35:26,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d7dd77-f3f5-4234-b381-10a56e3fe66c/GCA_011321845.1_ASM1132184v1_genomic.fna.gz --refList GCA_011321845.1_ASM1132184v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011321845.1_ASM1132184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:35:39,096] [INFO] Task succeeded: fastANI
[2023-06-29 19:35:39,105] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:35:39,105] [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_011321845.1	s__HyVt-539 sp011321845	100.0	1228	1243	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__GCA-002748355;g__HyVt-539	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002748355.1	s__GCA-2748355 sp002748355	76.2823	56	1243	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__GCA-002748355;g__GCA-2748355	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:35:39,108] [INFO] GTDB search result was written to GCA_011321845.1_ASM1132184v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:35:39,108] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:35:39,112] [INFO] DFAST_QC result json was written to GCA_011321845.1_ASM1132184v1_genomic.fna/dqc_result.json
[2023-06-29 19:35:39,113] [INFO] DFAST_QC completed!
[2023-06-29 19:35:39,113] [INFO] Total running time: 0h1m15s