[2023-06-28 22:57:15,625] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:57:15,628] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:57:15,628] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference
[2023-06-28 22:57:16,833] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:57:16,834] [INFO] Task started: Prodigal
[2023-06-28 22:57:16,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d44f995-3b6c-43e2-a6a1-29c74edce076/GCA_027310855.1_ASM2731085v1_genomic.fna.gz | prodigal -d GCA_027310855.1_ASM2731085v1_genomic.fna/cds.fna -a GCA_027310855.1_ASM2731085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:57:27,015] [INFO] Task succeeded: Prodigal
[2023-06-28 22:57:27,016] [INFO] Task started: HMMsearch
[2023-06-28 22:57:27,016] [INFO] Running command: hmmsearch --tblout GCA_027310855.1_ASM2731085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference/reference_markers.hmm GCA_027310855.1_ASM2731085v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:57:27,225] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:57:27,227] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3d44f995-3b6c-43e2-a6a1-29c74edce076/GCA_027310855.1_ASM2731085v1_genomic.fna.gz]
[2023-06-28 22:57:27,254] [INFO] Query marker FASTA was written to GCA_027310855.1_ASM2731085v1_genomic.fna/markers.fasta
[2023-06-28 22:57:27,255] [INFO] Task started: Blastn
[2023-06-28 22:57:27,255] [INFO] Running command: blastn -query GCA_027310855.1_ASM2731085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference/reference_markers.fasta -out GCA_027310855.1_ASM2731085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:57:27,742] [INFO] Task succeeded: Blastn
[2023-06-28 22:57:27,746] [INFO] Selected 5 target genomes.
[2023-06-28 22:57:27,746] [INFO] Target genome list was writen to GCA_027310855.1_ASM2731085v1_genomic.fna/target_genomes.txt
[2023-06-28 22:57:27,749] [INFO] Task started: fastANI
[2023-06-28 22:57:27,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d44f995-3b6c-43e2-a6a1-29c74edce076/GCA_027310855.1_ASM2731085v1_genomic.fna.gz --refList GCA_027310855.1_ASM2731085v1_genomic.fna/target_genomes.txt --output GCA_027310855.1_ASM2731085v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:57:31,801] [INFO] Task succeeded: fastANI
[2023-06-28 22:57:31,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:57:31,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:57:31,808] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:57:31,808] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:57:31,808] [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
Pseudonocardia xinjiangensis	strain=JCM 11839	GCA_012911925.1	75289	75289	type	True	74.526	51	680	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:57:31,811] [INFO] DFAST Taxonomy check result was written to GCA_027310855.1_ASM2731085v1_genomic.fna/tc_result.tsv
[2023-06-28 22:57:31,811] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:57:31,811] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:57:31,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference/checkm_data
[2023-06-28 22:57:31,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:57:31,842] [INFO] Task started: CheckM
[2023-06-28 22:57:31,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310855.1_ASM2731085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310855.1_ASM2731085v1_genomic.fna/checkm_input GCA_027310855.1_ASM2731085v1_genomic.fna/checkm_result
[2023-06-28 22:58:03,773] [INFO] Task succeeded: CheckM
[2023-06-28 22:58:03,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:58:03,799] [INFO] ===== Completeness check finished =====
[2023-06-28 22:58:03,799] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:58:03,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310855.1_ASM2731085v1_genomic.fna/markers.fasta)
[2023-06-28 22:58:03,800] [INFO] Task started: Blastn
[2023-06-28 22:58:03,800] [INFO] Running command: blastn -query GCA_027310855.1_ASM2731085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbb000b0-5c3b-4ae1-9295-c2d9910ebf8c/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310855.1_ASM2731085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:58:04,288] [INFO] Task succeeded: Blastn
[2023-06-28 22:58:04,292] [INFO] Selected 5 target genomes.
[2023-06-28 22:58:04,293] [INFO] Target genome list was writen to GCA_027310855.1_ASM2731085v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:58:04,294] [INFO] Task started: fastANI
[2023-06-28 22:58:04,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d44f995-3b6c-43e2-a6a1-29c74edce076/GCA_027310855.1_ASM2731085v1_genomic.fna.gz --refList GCA_027310855.1_ASM2731085v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310855.1_ASM2731085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:58:05,788] [INFO] Task succeeded: fastANI
[2023-06-28 22:58:05,796] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 22:58:05,796] [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_002503985.1	s__UBA184 sp002503985	78.9812	220	680	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495185.1	s__UBA184 sp002495185	78.3669	209	680	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044425.1	s__UBA184 sp013044425	77.2969	119	680	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:58:05,798] [INFO] GTDB search result was written to GCA_027310855.1_ASM2731085v1_genomic.fna/result_gtdb.tsv
[2023-06-28 22:58:05,799] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:58:05,802] [INFO] DFAST_QC result json was written to GCA_027310855.1_ASM2731085v1_genomic.fna/dqc_result.json
[2023-06-28 22:58:05,802] [INFO] DFAST_QC completed!
[2023-06-28 22:58:05,802] [INFO] Total running time: 0h0m50s