[2023-06-13 15:27:22,424] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:27:22,427] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:27:22,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference
[2023-06-13 15:27:24,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:27:24,047] [INFO] Task started: Prodigal
[2023-06-13 15:27:24,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg10c6f6c5-3674-4daa-960e-01138e7b02a9/GCA_022508535.1_ASM2250853v1_genomic.fna.gz | prodigal -d GCA_022508535.1_ASM2250853v1_genomic.fna/cds.fna -a GCA_022508535.1_ASM2250853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:27:26,689] [INFO] Task succeeded: Prodigal
[2023-06-13 15:27:26,690] [INFO] Task started: HMMsearch
[2023-06-13 15:27:26,690] [INFO] Running command: hmmsearch --tblout GCA_022508535.1_ASM2250853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference/reference_markers.hmm GCA_022508535.1_ASM2250853v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:27:26,934] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:27:26,935] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10c6f6c5-3674-4daa-960e-01138e7b02a9/GCA_022508535.1_ASM2250853v1_genomic.fna.gz]
[2023-06-13 15:27:26,958] [INFO] Query marker FASTA was written to GCA_022508535.1_ASM2250853v1_genomic.fna/markers.fasta
[2023-06-13 15:27:26,959] [INFO] Task started: Blastn
[2023-06-13 15:27:26,959] [INFO] Running command: blastn -query GCA_022508535.1_ASM2250853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference/reference_markers.fasta -out GCA_022508535.1_ASM2250853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:27,538] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:27,543] [INFO] Selected 20 target genomes.
[2023-06-13 15:27:27,544] [INFO] Target genome list was writen to GCA_022508535.1_ASM2250853v1_genomic.fna/target_genomes.txt
[2023-06-13 15:27:27,552] [INFO] Task started: fastANI
[2023-06-13 15:27:27,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg10c6f6c5-3674-4daa-960e-01138e7b02a9/GCA_022508535.1_ASM2250853v1_genomic.fna.gz --refList GCA_022508535.1_ASM2250853v1_genomic.fna/target_genomes.txt --output GCA_022508535.1_ASM2250853v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:27:36,116] [INFO] Task succeeded: fastANI
[2023-06-13 15:27:36,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:27:36,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:27:36,120] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:27:36,120] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 15:27:36,121] [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
--------------------------------------------------------------------------------
[2023-06-13 15:27:36,123] [INFO] DFAST Taxonomy check result was written to GCA_022508535.1_ASM2250853v1_genomic.fna/tc_result.tsv
[2023-06-13 15:27:36,123] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:27:36,124] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:27:36,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference/checkm_data
[2023-06-13 15:27:36,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:27:36,165] [INFO] Task started: CheckM
[2023-06-13 15:27:36,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022508535.1_ASM2250853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022508535.1_ASM2250853v1_genomic.fna/checkm_input GCA_022508535.1_ASM2250853v1_genomic.fna/checkm_result
[2023-06-13 15:27:53,262] [INFO] Task succeeded: CheckM
[2023-06-13 15:27:53,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:27:53,295] [INFO] ===== Completeness check finished =====
[2023-06-13 15:27:53,295] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:27:53,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022508535.1_ASM2250853v1_genomic.fna/markers.fasta)
[2023-06-13 15:27:53,296] [INFO] Task started: Blastn
[2023-06-13 15:27:53,296] [INFO] Running command: blastn -query GCA_022508535.1_ASM2250853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90391856-6040-402f-ba0e-dd0dd98172b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022508535.1_ASM2250853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:54,063] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:54,069] [INFO] Selected 16 target genomes.
[2023-06-13 15:27:54,069] [INFO] Target genome list was writen to GCA_022508535.1_ASM2250853v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:27:54,081] [INFO] Task started: fastANI
[2023-06-13 15:27:54,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg10c6f6c5-3674-4daa-960e-01138e7b02a9/GCA_022508535.1_ASM2250853v1_genomic.fna.gz --refList GCA_022508535.1_ASM2250853v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022508535.1_ASM2250853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:27:58,593] [INFO] Task succeeded: fastANI
[2023-06-13 15:27:58,599] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:27:58,599] [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_900315885.1	s__RUG131 sp900315885	79.6796	142	482	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__RUG131	95.0	98.82	98.20	0.90	0.84	4	-
GCA_900549975.1	s__RUG131 sp900549975	79.3233	115	482	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__RUG131	95.0	99.95	99.90	0.93	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-13 15:27:58,602] [INFO] GTDB search result was written to GCA_022508535.1_ASM2250853v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:27:58,603] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:27:58,607] [INFO] DFAST_QC result json was written to GCA_022508535.1_ASM2250853v1_genomic.fna/dqc_result.json
[2023-06-13 15:27:58,607] [INFO] DFAST_QC completed!
[2023-06-13 15:27:58,607] [INFO] Total running time: 0h0m36s