[2023-06-27 15:56:35,645] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:56:35,647] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:56:35,647] [INFO] DQC Reference Directory: /var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference
[2023-06-27 15:56:36,755] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:56:36,756] [INFO] Task started: Prodigal
[2023-06-27 15:56:36,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg30fa4f4e-75df-4b71-9f60-4de3933f34da/GCA_026710155.1_ASM2671015v1_genomic.fna.gz | prodigal -d GCA_026710155.1_ASM2671015v1_genomic.fna/cds.fna -a GCA_026710155.1_ASM2671015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:56:44,229] [INFO] Task succeeded: Prodigal
[2023-06-27 15:56:44,229] [INFO] Task started: HMMsearch
[2023-06-27 15:56:44,229] [INFO] Running command: hmmsearch --tblout GCA_026710155.1_ASM2671015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference/reference_markers.hmm GCA_026710155.1_ASM2671015v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:56:44,406] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:56:44,408] [INFO] Found 6/6 markers.
[2023-06-27 15:56:44,433] [INFO] Query marker FASTA was written to GCA_026710155.1_ASM2671015v1_genomic.fna/markers.fasta
[2023-06-27 15:56:44,433] [INFO] Task started: Blastn
[2023-06-27 15:56:44,433] [INFO] Running command: blastn -query GCA_026710155.1_ASM2671015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference/reference_markers.fasta -out GCA_026710155.1_ASM2671015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:56:45,007] [INFO] Task succeeded: Blastn
[2023-06-27 15:56:45,010] [INFO] Selected 29 target genomes.
[2023-06-27 15:56:45,010] [INFO] Target genome list was writen to GCA_026710155.1_ASM2671015v1_genomic.fna/target_genomes.txt
[2023-06-27 15:56:45,015] [INFO] Task started: fastANI
[2023-06-27 15:56:45,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg30fa4f4e-75df-4b71-9f60-4de3933f34da/GCA_026710155.1_ASM2671015v1_genomic.fna.gz --refList GCA_026710155.1_ASM2671015v1_genomic.fna/target_genomes.txt --output GCA_026710155.1_ASM2671015v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 15:57:03,009] [INFO] Task succeeded: fastANI
[2023-06-27 15:57:03,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 15:57:03,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 15:57:03,011] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 15:57:03,011] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 15:57:03,011] [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
--------------------------------------------------------------------------------
[2023-06-27 15:57:03,013] [INFO] DFAST Taxonomy check result was written to GCA_026710155.1_ASM2671015v1_genomic.fna/tc_result.tsv
[2023-06-27 15:57:03,014] [INFO] ===== Taxonomy check completed =====
[2023-06-27 15:57:03,014] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:57:03,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference/checkm_data
[2023-06-27 15:57:03,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:57:03,048] [INFO] Task started: CheckM
[2023-06-27 15:57:03,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026710155.1_ASM2671015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026710155.1_ASM2671015v1_genomic.fna/checkm_input GCA_026710155.1_ASM2671015v1_genomic.fna/checkm_result
[2023-06-27 15:57:29,286] [INFO] Task succeeded: CheckM
[2023-06-27 15:57:29,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 15:57:29,306] [INFO] ===== Completeness check finished =====
[2023-06-27 15:57:29,306] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:57:29,307] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026710155.1_ASM2671015v1_genomic.fna/markers.fasta)
[2023-06-27 15:57:29,307] [INFO] Task started: Blastn
[2023-06-27 15:57:29,307] [INFO] Running command: blastn -query GCA_026710155.1_ASM2671015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3874c75-9784-4b7a-be65-1f0d39fccf6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_026710155.1_ASM2671015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:57:30,256] [INFO] Task succeeded: Blastn
[2023-06-27 15:57:30,260] [INFO] Selected 19 target genomes.
[2023-06-27 15:57:30,260] [INFO] Target genome list was writen to GCA_026710155.1_ASM2671015v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:57:30,267] [INFO] Task started: fastANI
[2023-06-27 15:57:30,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg30fa4f4e-75df-4b71-9f60-4de3933f34da/GCA_026710155.1_ASM2671015v1_genomic.fna.gz --refList GCA_026710155.1_ASM2671015v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026710155.1_ASM2671015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:57:40,371] [INFO] Task succeeded: fastANI
[2023-06-27 15:57:40,374] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:57:40,374] [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_009842205.1	s__MPNP01 sp009842205	88.5583	737	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MPNP01	95.0	98.85	97.48	0.96	0.94	5	-
GCA_011523445.1	s__MPNP01 sp011523445	88.205	527	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MPNP01	95.0	96.79	96.63	0.76	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-27 15:57:40,376] [INFO] GTDB search result was written to GCA_026710155.1_ASM2671015v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:57:40,376] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:57:40,380] [INFO] DFAST_QC result json was written to GCA_026710155.1_ASM2671015v1_genomic.fna/dqc_result.json
[2023-06-27 15:57:40,380] [INFO] DFAST_QC completed!
[2023-06-27 15:57:40,380] [INFO] Total running time: 0h1m5s