[2023-06-28 23:39:53,509] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:39:53,511] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:39:53,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference
[2023-06-28 23:39:54,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:39:54,908] [INFO] Task started: Prodigal
[2023-06-28 23:39:54,908] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3f4f98c-84b9-45f0-a986-b43f89e2aa16/GCA_017557765.1_ASM1755776v1_genomic.fna.gz | prodigal -d GCA_017557765.1_ASM1755776v1_genomic.fna/cds.fna -a GCA_017557765.1_ASM1755776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:40:00,060] [INFO] Task succeeded: Prodigal
[2023-06-28 23:40:00,061] [INFO] Task started: HMMsearch
[2023-06-28 23:40:00,061] [INFO] Running command: hmmsearch --tblout GCA_017557765.1_ASM1755776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference/reference_markers.hmm GCA_017557765.1_ASM1755776v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:40:00,315] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:40:00,317] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd3f4f98c-84b9-45f0-a986-b43f89e2aa16/GCA_017557765.1_ASM1755776v1_genomic.fna.gz]
[2023-06-28 23:40:00,347] [INFO] Query marker FASTA was written to GCA_017557765.1_ASM1755776v1_genomic.fna/markers.fasta
[2023-06-28 23:40:00,347] [INFO] Task started: Blastn
[2023-06-28 23:40:00,347] [INFO] Running command: blastn -query GCA_017557765.1_ASM1755776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference/reference_markers.fasta -out GCA_017557765.1_ASM1755776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:00,939] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:00,943] [INFO] Selected 17 target genomes.
[2023-06-28 23:40:00,944] [INFO] Target genome list was writen to GCA_017557765.1_ASM1755776v1_genomic.fna/target_genomes.txt
[2023-06-28 23:40:00,953] [INFO] Task started: fastANI
[2023-06-28 23:40:00,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3f4f98c-84b9-45f0-a986-b43f89e2aa16/GCA_017557765.1_ASM1755776v1_genomic.fna.gz --refList GCA_017557765.1_ASM1755776v1_genomic.fna/target_genomes.txt --output GCA_017557765.1_ASM1755776v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:40:15,364] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:15,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:40:15,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:40:15,367] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:40:15,367] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:40:15,367] [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 23:40:15,369] [INFO] DFAST Taxonomy check result was written to GCA_017557765.1_ASM1755776v1_genomic.fna/tc_result.tsv
[2023-06-28 23:40:15,370] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:40:15,370] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:40:15,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference/checkm_data
[2023-06-28 23:40:15,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:40:15,402] [INFO] Task started: CheckM
[2023-06-28 23:40:15,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017557765.1_ASM1755776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017557765.1_ASM1755776v1_genomic.fna/checkm_input GCA_017557765.1_ASM1755776v1_genomic.fna/checkm_result
[2023-06-28 23:40:38,104] [INFO] Task succeeded: CheckM
[2023-06-28 23:40:38,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.08%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 23:40:38,129] [INFO] ===== Completeness check finished =====
[2023-06-28 23:40:38,129] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:40:38,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017557765.1_ASM1755776v1_genomic.fna/markers.fasta)
[2023-06-28 23:40:38,130] [INFO] Task started: Blastn
[2023-06-28 23:40:38,130] [INFO] Running command: blastn -query GCA_017557765.1_ASM1755776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da98f60-ed4a-45bc-be71-78f15fefce2a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017557765.1_ASM1755776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:38,919] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:38,923] [INFO] Selected 9 target genomes.
[2023-06-28 23:40:38,924] [INFO] Target genome list was writen to GCA_017557765.1_ASM1755776v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:40:38,930] [INFO] Task started: fastANI
[2023-06-28 23:40:38,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3f4f98c-84b9-45f0-a986-b43f89e2aa16/GCA_017557765.1_ASM1755776v1_genomic.fna.gz --refList GCA_017557765.1_ASM1755776v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017557765.1_ASM1755776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:40:45,605] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:45,615] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:40:45,616] [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_017557195.1	s__RUG11551 sp017557195	89.4791	262	293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG11551	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017407125.1	s__RUG11551 sp017407125	89.0931	259	293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG11551	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447745.1	s__RUG11551 sp017447745	87.8976	253	293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG11551	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902770245.1	s__RUG11551 sp902770245	87.5412	257	293	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__RUG11551	95.0	95.54	95.49	0.88	0.88	3	-
--------------------------------------------------------------------------------
[2023-06-28 23:40:45,618] [INFO] GTDB search result was written to GCA_017557765.1_ASM1755776v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:40:45,619] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:40:45,622] [INFO] DFAST_QC result json was written to GCA_017557765.1_ASM1755776v1_genomic.fna/dqc_result.json
[2023-06-28 23:40:45,623] [INFO] DFAST_QC completed!
[2023-06-28 23:40:45,623] [INFO] Total running time: 0h0m52s