[2023-06-04 21:46:05,305] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:46:05,307] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:46:05,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference
[2023-06-04 21:46:06,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:46:06,600] [INFO] Task started: Prodigal
[2023-06-04 21:46:06,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ddc1f8b-1815-4c8a-99a0-6a2a66eeb5f5/GCA_010022685.1_ASM1002268v1_genomic.fna.gz | prodigal -d GCA_010022685.1_ASM1002268v1_genomic.fna/cds.fna -a GCA_010022685.1_ASM1002268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:46:09,347] [INFO] Task succeeded: Prodigal
[2023-06-04 21:46:09,348] [INFO] Task started: HMMsearch
[2023-06-04 21:46:09,348] [INFO] Running command: hmmsearch --tblout GCA_010022685.1_ASM1002268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference/reference_markers.hmm GCA_010022685.1_ASM1002268v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:46:09,573] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:46:09,574] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4ddc1f8b-1815-4c8a-99a0-6a2a66eeb5f5/GCA_010022685.1_ASM1002268v1_genomic.fna.gz]
[2023-06-04 21:46:09,594] [INFO] Query marker FASTA was written to GCA_010022685.1_ASM1002268v1_genomic.fna/markers.fasta
[2023-06-04 21:46:09,595] [INFO] Task started: Blastn
[2023-06-04 21:46:09,595] [INFO] Running command: blastn -query GCA_010022685.1_ASM1002268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference/reference_markers.fasta -out GCA_010022685.1_ASM1002268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:10,227] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:10,231] [INFO] Selected 11 target genomes.
[2023-06-04 21:46:10,232] [INFO] Target genome list was writen to GCA_010022685.1_ASM1002268v1_genomic.fna/target_genomes.txt
[2023-06-04 21:46:10,233] [INFO] Task started: fastANI
[2023-06-04 21:46:10,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ddc1f8b-1815-4c8a-99a0-6a2a66eeb5f5/GCA_010022685.1_ASM1002268v1_genomic.fna.gz --refList GCA_010022685.1_ASM1002268v1_genomic.fna/target_genomes.txt --output GCA_010022685.1_ASM1002268v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:46:14,145] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:14,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:46:14,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:46:14,152] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:46:14,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 21:46:14,152] [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
Polynucleobacter acidiphobus	strain=MWH-PoolGreenA3	GCA_003065385.1	556053	556053	type	True	85.6387	165	181	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 21:46:14,154] [INFO] DFAST Taxonomy check result was written to GCA_010022685.1_ASM1002268v1_genomic.fna/tc_result.tsv
[2023-06-04 21:46:14,154] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:46:14,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:46:14,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference/checkm_data
[2023-06-04 21:46:14,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:46:14,176] [INFO] Task started: CheckM
[2023-06-04 21:46:14,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010022685.1_ASM1002268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010022685.1_ASM1002268v1_genomic.fna/checkm_input GCA_010022685.1_ASM1002268v1_genomic.fna/checkm_result
[2023-06-04 21:46:30,521] [INFO] Task succeeded: CheckM
[2023-06-04 21:46:30,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:46:30,549] [INFO] ===== Completeness check finished =====
[2023-06-04 21:46:30,550] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:46:30,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010022685.1_ASM1002268v1_genomic.fna/markers.fasta)
[2023-06-04 21:46:30,550] [INFO] Task started: Blastn
[2023-06-04 21:46:30,550] [INFO] Running command: blastn -query GCA_010022685.1_ASM1002268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e7e5459-80ff-4d3d-960b-767bea700cfa/dqc_reference/reference_markers_gtdb.fasta -out GCA_010022685.1_ASM1002268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:46:31,443] [INFO] Task succeeded: Blastn
[2023-06-04 21:46:31,448] [INFO] Selected 12 target genomes.
[2023-06-04 21:46:31,448] [INFO] Target genome list was writen to GCA_010022685.1_ASM1002268v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:46:31,452] [INFO] Task started: fastANI
[2023-06-04 21:46:31,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ddc1f8b-1815-4c8a-99a0-6a2a66eeb5f5/GCA_010022685.1_ASM1002268v1_genomic.fna.gz --refList GCA_010022685.1_ASM1002268v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010022685.1_ASM1002268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:46:35,033] [INFO] Task succeeded: fastANI
[2023-06-04 21:46:35,043] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:46:35,044] [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
GCF_018687475.1	s__Polynucleobacter sp009928245	97.6389	174	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	97.52	97.29	0.97	0.94	13	conclusive
GCA_016867965.1	s__Polynucleobacter sp016867965	94.1095	161	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003065385.1	s__Polynucleobacter acidiphobus	85.6387	165	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292975.1	s__Polynucleobacter sp002292975	79.4032	65	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.75	98.63	0.92	0.90	4	-
GCA_009924985.1	s__Polynucleobacter sp009924985	79.2356	55	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359975.1	s__Polynucleobacter sp002359975	78.9256	55	181	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.53	97.93	0.70	0.67	7	-
--------------------------------------------------------------------------------
[2023-06-04 21:46:35,046] [INFO] GTDB search result was written to GCA_010022685.1_ASM1002268v1_genomic.fna/result_gtdb.tsv
[2023-06-04 21:46:35,046] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:46:35,048] [INFO] DFAST_QC result json was written to GCA_010022685.1_ASM1002268v1_genomic.fna/dqc_result.json
[2023-06-04 21:46:35,049] [INFO] DFAST_QC completed!
[2023-06-04 21:46:35,049] [INFO] Total running time: 0h0m30s