[2023-06-30 21:18:05,575] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:18:05,581] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:18:05,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference
[2023-06-30 21:18:07,298] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:18:07,299] [INFO] Task started: Prodigal
[2023-06-30 21:18:07,299] [INFO] Running command: gunzip -c /var/lib/cwl/stg2faaeb5f-faa2-4410-972e-bdddeb80408f/GCA_016708405.1_ASM1670840v1_genomic.fna.gz | prodigal -d GCA_016708405.1_ASM1670840v1_genomic.fna/cds.fna -a GCA_016708405.1_ASM1670840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:18:18,682] [INFO] Task succeeded: Prodigal
[2023-06-30 21:18:18,682] [INFO] Task started: HMMsearch
[2023-06-30 21:18:18,682] [INFO] Running command: hmmsearch --tblout GCA_016708405.1_ASM1670840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference/reference_markers.hmm GCA_016708405.1_ASM1670840v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:18:18,946] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:18:18,948] [INFO] Found 6/6 markers.
[2023-06-30 21:18:18,982] [INFO] Query marker FASTA was written to GCA_016708405.1_ASM1670840v1_genomic.fna/markers.fasta
[2023-06-30 21:18:18,983] [INFO] Task started: Blastn
[2023-06-30 21:18:18,983] [INFO] Running command: blastn -query GCA_016708405.1_ASM1670840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference/reference_markers.fasta -out GCA_016708405.1_ASM1670840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:18:19,596] [INFO] Task succeeded: Blastn
[2023-06-30 21:18:19,600] [INFO] Selected 23 target genomes.
[2023-06-30 21:18:19,600] [INFO] Target genome list was writen to GCA_016708405.1_ASM1670840v1_genomic.fna/target_genomes.txt
[2023-06-30 21:18:19,602] [INFO] Task started: fastANI
[2023-06-30 21:18:19,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg2faaeb5f-faa2-4410-972e-bdddeb80408f/GCA_016708405.1_ASM1670840v1_genomic.fna.gz --refList GCA_016708405.1_ASM1670840v1_genomic.fna/target_genomes.txt --output GCA_016708405.1_ASM1670840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:18:33,135] [INFO] Task succeeded: fastANI
[2023-06-30 21:18:33,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:18:33,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:18:33,137] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:18:33,137] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:18:33,137] [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
--------------------------------------------------------------------------------
[2023-06-30 21:18:33,138] [INFO] DFAST Taxonomy check result was written to GCA_016708405.1_ASM1670840v1_genomic.fna/tc_result.tsv
[2023-06-30 21:18:33,139] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:18:33,139] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:18:33,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference/checkm_data
[2023-06-30 21:18:33,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:18:33,181] [INFO] Task started: CheckM
[2023-06-30 21:18:33,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708405.1_ASM1670840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708405.1_ASM1670840v1_genomic.fna/checkm_input GCA_016708405.1_ASM1670840v1_genomic.fna/checkm_result
[2023-06-30 21:19:11,609] [INFO] Task succeeded: CheckM
[2023-06-30 21:19:11,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:19:11,630] [INFO] ===== Completeness check finished =====
[2023-06-30 21:19:11,631] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:19:11,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708405.1_ASM1670840v1_genomic.fna/markers.fasta)
[2023-06-30 21:19:11,631] [INFO] Task started: Blastn
[2023-06-30 21:19:11,632] [INFO] Running command: blastn -query GCA_016708405.1_ASM1670840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c8963be-b643-42e8-b6b3-71f429965e61/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708405.1_ASM1670840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:19:12,494] [INFO] Task succeeded: Blastn
[2023-06-30 21:19:12,499] [INFO] Selected 18 target genomes.
[2023-06-30 21:19:12,500] [INFO] Target genome list was writen to GCA_016708405.1_ASM1670840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:19:12,501] [INFO] Task started: fastANI
[2023-06-30 21:19:12,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg2faaeb5f-faa2-4410-972e-bdddeb80408f/GCA_016708405.1_ASM1670840v1_genomic.fna.gz --refList GCA_016708405.1_ASM1670840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708405.1_ASM1670840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:19:23,095] [INFO] Task succeeded: fastANI
[2023-06-30 21:19:23,109] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:19:23,109] [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_016707005.1	s__UBA10438 sp002426145	98.5046	1040	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__UBA10438	95.0	98.87	98.20	0.93	0.89	12	conclusive
GCA_903939735.1	s__UBA10438 sp903939735	78.0089	158	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__UBA10438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883125.1	s__UBA10438 sp018883125	76.9881	115	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__UBA10438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003488525.1	s__UBA10438 sp003488525	76.8951	96	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__UBA10438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882895.1	s__UBA10438 sp018882895	76.6458	104	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__UBA10438	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266735.1	s__Kapabacteria sp018266735	76.5978	114	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__Kapabacteria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899175.1	s__Kapabacteria thiocyanatum	76.364	94	1203	d__Bacteria;p__Bacteroidota;c__Kapabacteria;o__Kapabacteriales;f__Kapabacteriaceae;g__Kapabacteria	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-30 21:19:23,111] [INFO] GTDB search result was written to GCA_016708405.1_ASM1670840v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:19:23,112] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:19:23,114] [INFO] DFAST_QC result json was written to GCA_016708405.1_ASM1670840v1_genomic.fna/dqc_result.json
[2023-06-30 21:19:23,114] [INFO] DFAST_QC completed!
[2023-06-30 21:19:23,114] [INFO] Total running time: 0h1m18s