[2023-06-13 04:13:07,932] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:13:07,938] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:13:07,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference
[2023-06-13 04:13:09,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:13:09,322] [INFO] Task started: Prodigal
[2023-06-13 04:13:09,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg58d7458b-46bc-48a3-be2b-76f64ed22790/GCA_022708765.1_ASM2270876v1_genomic.fna.gz | prodigal -d GCA_022708765.1_ASM2270876v1_genomic.fna/cds.fna -a GCA_022708765.1_ASM2270876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:13:21,204] [INFO] Task succeeded: Prodigal
[2023-06-13 04:13:21,205] [INFO] Task started: HMMsearch
[2023-06-13 04:13:21,205] [INFO] Running command: hmmsearch --tblout GCA_022708765.1_ASM2270876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference/reference_markers.hmm GCA_022708765.1_ASM2270876v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:13:21,509] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:13:21,510] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg58d7458b-46bc-48a3-be2b-76f64ed22790/GCA_022708765.1_ASM2270876v1_genomic.fna.gz]
[2023-06-13 04:13:21,553] [INFO] Query marker FASTA was written to GCA_022708765.1_ASM2270876v1_genomic.fna/markers.fasta
[2023-06-13 04:13:21,553] [INFO] Task started: Blastn
[2023-06-13 04:13:21,553] [INFO] Running command: blastn -query GCA_022708765.1_ASM2270876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference/reference_markers.fasta -out GCA_022708765.1_ASM2270876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:13:22,096] [INFO] Task succeeded: Blastn
[2023-06-13 04:13:22,100] [INFO] Selected 18 target genomes.
[2023-06-13 04:13:22,100] [INFO] Target genome list was writen to GCA_022708765.1_ASM2270876v1_genomic.fna/target_genomes.txt
[2023-06-13 04:13:22,104] [INFO] Task started: fastANI
[2023-06-13 04:13:22,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d7458b-46bc-48a3-be2b-76f64ed22790/GCA_022708765.1_ASM2270876v1_genomic.fna.gz --refList GCA_022708765.1_ASM2270876v1_genomic.fna/target_genomes.txt --output GCA_022708765.1_ASM2270876v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:13:31,739] [INFO] Task succeeded: fastANI
[2023-06-13 04:13:31,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:13:31,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:13:31,744] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:13:31,745] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:13:31,745] [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
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	74.7532	51	1179	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:13:31,747] [INFO] DFAST Taxonomy check result was written to GCA_022708765.1_ASM2270876v1_genomic.fna/tc_result.tsv
[2023-06-13 04:13:31,747] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:13:31,748] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:13:31,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference/checkm_data
[2023-06-13 04:13:31,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:13:31,796] [INFO] Task started: CheckM
[2023-06-13 04:13:31,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708765.1_ASM2270876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708765.1_ASM2270876v1_genomic.fna/checkm_input GCA_022708765.1_ASM2270876v1_genomic.fna/checkm_result
[2023-06-13 04:14:09,664] [INFO] Task succeeded: CheckM
[2023-06-13 04:14:09,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:14:09,688] [INFO] ===== Completeness check finished =====
[2023-06-13 04:14:09,688] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:14:09,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708765.1_ASM2270876v1_genomic.fna/markers.fasta)
[2023-06-13 04:14:09,689] [INFO] Task started: Blastn
[2023-06-13 04:14:09,689] [INFO] Running command: blastn -query GCA_022708765.1_ASM2270876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c38af44-6aaf-4f17-9f29-be14a8d7039e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708765.1_ASM2270876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:14:10,137] [INFO] Task succeeded: Blastn
[2023-06-13 04:14:10,141] [INFO] Selected 20 target genomes.
[2023-06-13 04:14:10,141] [INFO] Target genome list was writen to GCA_022708765.1_ASM2270876v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:14:10,153] [INFO] Task started: fastANI
[2023-06-13 04:14:10,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg58d7458b-46bc-48a3-be2b-76f64ed22790/GCA_022708765.1_ASM2270876v1_genomic.fna.gz --refList GCA_022708765.1_ASM2270876v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708765.1_ASM2270876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:14:21,978] [INFO] Task succeeded: fastANI
[2023-06-13 04:14:21,983] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 04:14:21,983] [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_903928345.1	s__CAIYQO01 sp903928345	76.9695	226	1179	d__Bacteria;p__Armatimonadota;c__CAIYQO01;o__CAIYQO01;f__CAIYQO01;g__CAIYQO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:14:21,986] [INFO] GTDB search result was written to GCA_022708765.1_ASM2270876v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:14:21,987] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:14:22,004] [INFO] DFAST_QC result json was written to GCA_022708765.1_ASM2270876v1_genomic.fna/dqc_result.json
[2023-06-13 04:14:22,005] [INFO] DFAST_QC completed!
[2023-06-13 04:14:22,005] [INFO] Total running time: 0h1m14s