[2023-06-28 05:22:36,295] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:22:36,299] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:22:36,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference
[2023-06-28 05:22:37,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:22:37,678] [INFO] Task started: Prodigal
[2023-06-28 05:22:37,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg81e6c9df-e634-4c72-b314-31069c8f10b5/GCA_017628105.1_ASM1762810v1_genomic.fna.gz | prodigal -d GCA_017628105.1_ASM1762810v1_genomic.fna/cds.fna -a GCA_017628105.1_ASM1762810v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:22:39,087] [INFO] Task succeeded: Prodigal
[2023-06-28 05:22:39,087] [INFO] Task started: HMMsearch
[2023-06-28 05:22:39,087] [INFO] Running command: hmmsearch --tblout GCA_017628105.1_ASM1762810v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference/reference_markers.hmm GCA_017628105.1_ASM1762810v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:22:39,239] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:22:39,240] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg81e6c9df-e634-4c72-b314-31069c8f10b5/GCA_017628105.1_ASM1762810v1_genomic.fna.gz]
[2023-06-28 05:22:39,263] [INFO] Query marker FASTA was written to GCA_017628105.1_ASM1762810v1_genomic.fna/markers.fasta
[2023-06-28 05:22:39,264] [INFO] Task started: Blastn
[2023-06-28 05:22:39,264] [INFO] Running command: blastn -query GCA_017628105.1_ASM1762810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference/reference_markers.fasta -out GCA_017628105.1_ASM1762810v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:22:39,778] [INFO] Task succeeded: Blastn
[2023-06-28 05:22:39,787] [INFO] Selected 5 target genomes.
[2023-06-28 05:22:39,787] [INFO] Target genome list was writen to GCA_017628105.1_ASM1762810v1_genomic.fna/target_genomes.txt
[2023-06-28 05:22:39,788] [INFO] Task started: fastANI
[2023-06-28 05:22:39,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e6c9df-e634-4c72-b314-31069c8f10b5/GCA_017628105.1_ASM1762810v1_genomic.fna.gz --refList GCA_017628105.1_ASM1762810v1_genomic.fna/target_genomes.txt --output GCA_017628105.1_ASM1762810v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:22:42,709] [INFO] Task succeeded: fastANI
[2023-06-28 05:22:42,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:22:42,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:22:42,711] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:22:42,711] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:22:42,712] [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
--------------------------------------------------------------------------------
[2023-06-28 05:22:42,713] [INFO] DFAST Taxonomy check result was written to GCA_017628105.1_ASM1762810v1_genomic.fna/tc_result.tsv
[2023-06-28 05:22:42,714] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:22:42,714] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:22:42,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference/checkm_data
[2023-06-28 05:22:42,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:22:42,729] [INFO] Task started: CheckM
[2023-06-28 05:22:42,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017628105.1_ASM1762810v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017628105.1_ASM1762810v1_genomic.fna/checkm_input GCA_017628105.1_ASM1762810v1_genomic.fna/checkm_result
[2023-06-28 05:22:55,761] [INFO] Task succeeded: CheckM
[2023-06-28 05:22:55,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 5.21%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-06-28 05:22:55,782] [INFO] ===== Completeness check finished =====
[2023-06-28 05:22:55,782] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:22:55,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017628105.1_ASM1762810v1_genomic.fna/markers.fasta)
[2023-06-28 05:22:55,782] [INFO] Task started: Blastn
[2023-06-28 05:22:55,783] [INFO] Running command: blastn -query GCA_017628105.1_ASM1762810v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f406f3b-b29b-4d85-9fa8-57a2639643c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_017628105.1_ASM1762810v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:22:56,674] [INFO] Task succeeded: Blastn
[2023-06-28 05:22:56,678] [INFO] Selected 11 target genomes.
[2023-06-28 05:22:56,678] [INFO] Target genome list was writen to GCA_017628105.1_ASM1762810v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:22:56,687] [INFO] Task started: fastANI
[2023-06-28 05:22:56,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg81e6c9df-e634-4c72-b314-31069c8f10b5/GCA_017628105.1_ASM1762810v1_genomic.fna.gz --refList GCA_017628105.1_ASM1762810v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017628105.1_ASM1762810v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:22:59,933] [INFO] Task succeeded: fastANI
[2023-06-28 05:22:59,939] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:22:59,939] [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_017508065.1	s__SIG5 sp017508065	90.6508	111	129	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__SIG5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063185.1	s__SIG5 sp015063185	83.8046	101	129	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__SIG5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297775.1	s__SIG5 sp016297775	83.0965	91	129	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__SIG5	95.0	98.79	98.79	0.83	0.83	2	-
GCA_016296195.1	s__UBA71 sp016296195	80.1987	53	129	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017395275.1	s__SIG5 sp017395275	79.4119	55	129	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__SIG5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:22:59,941] [INFO] GTDB search result was written to GCA_017628105.1_ASM1762810v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:22:59,942] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:22:59,944] [INFO] DFAST_QC result json was written to GCA_017628105.1_ASM1762810v1_genomic.fna/dqc_result.json
[2023-06-28 05:22:59,944] [INFO] DFAST_QC completed!
[2023-06-28 05:22:59,944] [INFO] Total running time: 0h0m24s