[2023-06-19 12:10:16,939] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:16,942] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:16,942] [INFO] DQC Reference Directory: /var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference
[2023-06-19 12:10:18,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:18,297] [INFO] Task started: Prodigal
[2023-06-19 12:10:18,297] [INFO] Running command: gunzip -c /var/lib/cwl/stgc982f08e-35b6-48d8-9985-bf0c0d1de197/GCA_018660145.1_ASM1866014v1_genomic.fna.gz | prodigal -d GCA_018660145.1_ASM1866014v1_genomic.fna/cds.fna -a GCA_018660145.1_ASM1866014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:22,295] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:22,295] [INFO] Task started: HMMsearch
[2023-06-19 12:10:22,295] [INFO] Running command: hmmsearch --tblout GCA_018660145.1_ASM1866014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference/reference_markers.hmm GCA_018660145.1_ASM1866014v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:22,505] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:22,507] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc982f08e-35b6-48d8-9985-bf0c0d1de197/GCA_018660145.1_ASM1866014v1_genomic.fna.gz]
[2023-06-19 12:10:22,530] [INFO] Query marker FASTA was written to GCA_018660145.1_ASM1866014v1_genomic.fna/markers.fasta
[2023-06-19 12:10:22,530] [INFO] Task started: Blastn
[2023-06-19 12:10:22,530] [INFO] Running command: blastn -query GCA_018660145.1_ASM1866014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference/reference_markers.fasta -out GCA_018660145.1_ASM1866014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:23,141] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:23,145] [INFO] Selected 23 target genomes.
[2023-06-19 12:10:23,146] [INFO] Target genome list was writen to GCA_018660145.1_ASM1866014v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:23,151] [INFO] Task started: fastANI
[2023-06-19 12:10:23,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgc982f08e-35b6-48d8-9985-bf0c0d1de197/GCA_018660145.1_ASM1866014v1_genomic.fna.gz --refList GCA_018660145.1_ASM1866014v1_genomic.fna/target_genomes.txt --output GCA_018660145.1_ASM1866014v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:10:36,599] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:36,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:10:36,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:10:36,601] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:10:36,601] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:10:36,602] [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
--------------------------------------------------------------------------------
[2023-06-19 12:10:36,603] [INFO] DFAST Taxonomy check result was written to GCA_018660145.1_ASM1866014v1_genomic.fna/tc_result.tsv
[2023-06-19 12:10:36,604] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:10:36,604] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:36,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference/checkm_data
[2023-06-19 12:10:36,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:36,630] [INFO] Task started: CheckM
[2023-06-19 12:10:36,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018660145.1_ASM1866014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018660145.1_ASM1866014v1_genomic.fna/checkm_input GCA_018660145.1_ASM1866014v1_genomic.fna/checkm_result
[2023-06-19 12:10:57,007] [INFO] Task succeeded: CheckM
[2023-06-19 12:10:57,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.81%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 12:10:57,037] [INFO] ===== Completeness check finished =====
[2023-06-19 12:10:57,037] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:10:57,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018660145.1_ASM1866014v1_genomic.fna/markers.fasta)
[2023-06-19 12:10:57,038] [INFO] Task started: Blastn
[2023-06-19 12:10:57,038] [INFO] Running command: blastn -query GCA_018660145.1_ASM1866014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb05bc228-3c38-43e0-bbde-656040c4c67a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018660145.1_ASM1866014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:58,030] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:58,033] [INFO] Selected 17 target genomes.
[2023-06-19 12:10:58,034] [INFO] Target genome list was writen to GCA_018660145.1_ASM1866014v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:10:58,041] [INFO] Task started: fastANI
[2023-06-19 12:10:58,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgc982f08e-35b6-48d8-9985-bf0c0d1de197/GCA_018660145.1_ASM1866014v1_genomic.fna.gz --refList GCA_018660145.1_ASM1866014v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018660145.1_ASM1866014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:11:05,628] [INFO] Task succeeded: fastANI
[2023-06-19 12:11:05,635] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:11:05,635] [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_018666295.1	s__Luminiphilus sp018666295	99.232	372	428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.15	99.01	0.84	0.82	4	conclusive
GCA_002390485.1	s__Luminiphilus sp002390485	94.7505	388	428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.01	96.90	0.92	0.88	5	-
GCA_000227505.4	s__Luminiphilus sp000227505	77.2912	56	428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	77.1696	78	428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524755.1	s__Luminiphilus sp011524755	76.9797	62	428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_002862405.1	s__Luminiphilus sp002862405	76.6635	72	428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
--------------------------------------------------------------------------------
[2023-06-19 12:11:05,637] [INFO] GTDB search result was written to GCA_018660145.1_ASM1866014v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:11:05,637] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:11:05,640] [INFO] DFAST_QC result json was written to GCA_018660145.1_ASM1866014v1_genomic.fna/dqc_result.json
[2023-06-19 12:11:05,640] [INFO] DFAST_QC completed!
[2023-06-19 12:11:05,640] [INFO] Total running time: 0h0m49s