[2023-06-13 06:44:33,030] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:44:33,032] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:44:33,033] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference
[2023-06-13 06:44:34,322] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:44:34,323] [INFO] Task started: Prodigal
[2023-06-13 06:44:34,323] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7af0706-c894-4587-8d7d-9a8e817616db/GCA_022425105.1_ASM2242510v1_genomic.fna.gz | prodigal -d GCA_022425105.1_ASM2242510v1_genomic.fna/cds.fna -a GCA_022425105.1_ASM2242510v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:44:40,704] [INFO] Task succeeded: Prodigal
[2023-06-13 06:44:40,705] [INFO] Task started: HMMsearch
[2023-06-13 06:44:40,705] [INFO] Running command: hmmsearch --tblout GCA_022425105.1_ASM2242510v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference/reference_markers.hmm GCA_022425105.1_ASM2242510v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:44:40,967] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:44:40,968] [INFO] Found 6/6 markers.
[2023-06-13 06:44:40,996] [INFO] Query marker FASTA was written to GCA_022425105.1_ASM2242510v1_genomic.fna/markers.fasta
[2023-06-13 06:44:40,996] [INFO] Task started: Blastn
[2023-06-13 06:44:40,996] [INFO] Running command: blastn -query GCA_022425105.1_ASM2242510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference/reference_markers.fasta -out GCA_022425105.1_ASM2242510v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:44:41,628] [INFO] Task succeeded: Blastn
[2023-06-13 06:44:41,633] [INFO] Selected 28 target genomes.
[2023-06-13 06:44:41,633] [INFO] Target genome list was writen to GCA_022425105.1_ASM2242510v1_genomic.fna/target_genomes.txt
[2023-06-13 06:44:41,641] [INFO] Task started: fastANI
[2023-06-13 06:44:41,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7af0706-c894-4587-8d7d-9a8e817616db/GCA_022425105.1_ASM2242510v1_genomic.fna.gz --refList GCA_022425105.1_ASM2242510v1_genomic.fna/target_genomes.txt --output GCA_022425105.1_ASM2242510v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:44:57,481] [INFO] Task succeeded: fastANI
[2023-06-13 06:44:57,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:44:57,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:44:57,483] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 06:44:57,483] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 06:44:57,483] [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
--------------------------------------------------------------------------------
[2023-06-13 06:44:57,485] [INFO] DFAST Taxonomy check result was written to GCA_022425105.1_ASM2242510v1_genomic.fna/tc_result.tsv
[2023-06-13 06:44:57,486] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:44:57,486] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:44:57,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference/checkm_data
[2023-06-13 06:44:57,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:44:57,521] [INFO] Task started: CheckM
[2023-06-13 06:44:57,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425105.1_ASM2242510v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425105.1_ASM2242510v1_genomic.fna/checkm_input GCA_022425105.1_ASM2242510v1_genomic.fna/checkm_result
[2023-06-13 06:45:23,511] [INFO] Task succeeded: CheckM
[2023-06-13 06:45:23,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 06:45:23,535] [INFO] ===== Completeness check finished =====
[2023-06-13 06:45:23,536] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:45:23,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425105.1_ASM2242510v1_genomic.fna/markers.fasta)
[2023-06-13 06:45:23,537] [INFO] Task started: Blastn
[2023-06-13 06:45:23,537] [INFO] Running command: blastn -query GCA_022425105.1_ASM2242510v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd6ca860-0d18-4c87-9f17-3b13d149fadc/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425105.1_ASM2242510v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:45:24,555] [INFO] Task succeeded: Blastn
[2023-06-13 06:45:24,573] [INFO] Selected 13 target genomes.
[2023-06-13 06:45:24,574] [INFO] Target genome list was writen to GCA_022425105.1_ASM2242510v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:45:24,585] [INFO] Task started: fastANI
[2023-06-13 06:45:24,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7af0706-c894-4587-8d7d-9a8e817616db/GCA_022425105.1_ASM2242510v1_genomic.fna.gz --refList GCA_022425105.1_ASM2242510v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425105.1_ASM2242510v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:45:29,904] [INFO] Task succeeded: fastANI
[2023-06-13 06:45:29,919] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:45:29,920] [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_009937065.1	s__Luminiphilus sp009937065	98.0697	608	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011524755.1	s__Luminiphilus sp011524755	82.5902	376	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_003523185.1	s__Luminiphilus sp003523185	82.1088	520	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547755.1	s__Luminiphilus sp902547755	81.9254	428	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613175.1	s__Luminiphilus sp902613175	81.917	364	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691565.1	s__Luminiphilus sp002691565	81.8665	368	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
GCA_002862405.1	s__Luminiphilus sp002862405	81.4032	475	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_002469785.1	s__Luminiphilus sp002469785	80.6341	369	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689915.1	s__Luminiphilus sp002689915	78.0154	113	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-13 06:45:29,921] [INFO] GTDB search result was written to GCA_022425105.1_ASM2242510v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:45:29,922] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:45:29,925] [INFO] DFAST_QC result json was written to GCA_022425105.1_ASM2242510v1_genomic.fna/dqc_result.json
[2023-06-13 06:45:29,925] [INFO] DFAST_QC completed!
[2023-06-13 06:45:29,925] [INFO] Total running time: 0h0m57s