[2023-06-04 21:56:06,285] [INFO] DFAST_QC pipeline started.
[2023-06-04 21:56:06,288] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 21:56:06,288] [INFO] DQC Reference Directory: /var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference
[2023-06-04 21:56:07,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 21:56:07,470] [INFO] Task started: Prodigal
[2023-06-04 21:56:07,470] [INFO] Running command: gunzip -c /var/lib/cwl/stga6b517e3-3c16-4985-bd06-1c6d76f7b36f/GCA_902517275.1_AG-325-O10_genomic.fna.gz | prodigal -d GCA_902517275.1_AG-325-O10_genomic.fna/cds.fna -a GCA_902517275.1_AG-325-O10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 21:56:09,359] [INFO] Task succeeded: Prodigal
[2023-06-04 21:56:09,360] [INFO] Task started: HMMsearch
[2023-06-04 21:56:09,360] [INFO] Running command: hmmsearch --tblout GCA_902517275.1_AG-325-O10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference/reference_markers.hmm GCA_902517275.1_AG-325-O10_genomic.fna/protein.faa > /dev/null
[2023-06-04 21:56:09,554] [INFO] Task succeeded: HMMsearch
[2023-06-04 21:56:09,556] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga6b517e3-3c16-4985-bd06-1c6d76f7b36f/GCA_902517275.1_AG-325-O10_genomic.fna.gz]
[2023-06-04 21:56:09,574] [INFO] Query marker FASTA was written to GCA_902517275.1_AG-325-O10_genomic.fna/markers.fasta
[2023-06-04 21:56:09,574] [INFO] Task started: Blastn
[2023-06-04 21:56:09,575] [INFO] Running command: blastn -query GCA_902517275.1_AG-325-O10_genomic.fna/markers.fasta -db /var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference/reference_markers.fasta -out GCA_902517275.1_AG-325-O10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:56:10,033] [INFO] Task succeeded: Blastn
[2023-06-04 21:56:10,043] [INFO] Selected 5 target genomes.
[2023-06-04 21:56:10,044] [INFO] Target genome list was writen to GCA_902517275.1_AG-325-O10_genomic.fna/target_genomes.txt
[2023-06-04 21:56:10,045] [INFO] Task started: fastANI
[2023-06-04 21:56:10,045] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b517e3-3c16-4985-bd06-1c6d76f7b36f/GCA_902517275.1_AG-325-O10_genomic.fna.gz --refList GCA_902517275.1_AG-325-O10_genomic.fna/target_genomes.txt --output GCA_902517275.1_AG-325-O10_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 21:56:11,786] [INFO] Task succeeded: fastANI
[2023-06-04 21:56:11,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 21:56:11,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 21:56:11,788] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 21:56:11,788] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 21:56:11,788] [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
--------------------------------------------------------------------------------
[2023-06-04 21:56:11,790] [INFO] DFAST Taxonomy check result was written to GCA_902517275.1_AG-325-O10_genomic.fna/tc_result.tsv
[2023-06-04 21:56:11,791] [INFO] ===== Taxonomy check completed =====
[2023-06-04 21:56:11,791] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 21:56:11,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference/checkm_data
[2023-06-04 21:56:11,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 21:56:11,812] [INFO] Task started: CheckM
[2023-06-04 21:56:11,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902517275.1_AG-325-O10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902517275.1_AG-325-O10_genomic.fna/checkm_input GCA_902517275.1_AG-325-O10_genomic.fna/checkm_result
[2023-06-04 21:56:25,521] [INFO] Task succeeded: CheckM
[2023-06-04 21:56:25,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 21:56:25,543] [INFO] ===== Completeness check finished =====
[2023-06-04 21:56:25,543] [INFO] ===== Start GTDB Search =====
[2023-06-04 21:56:25,544] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902517275.1_AG-325-O10_genomic.fna/markers.fasta)
[2023-06-04 21:56:25,544] [INFO] Task started: Blastn
[2023-06-04 21:56:25,544] [INFO] Running command: blastn -query GCA_902517275.1_AG-325-O10_genomic.fna/markers.fasta -db /var/lib/cwl/stg19a9d2f8-a033-4fbe-9cc2-53d7181782ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_902517275.1_AG-325-O10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 21:56:25,962] [INFO] Task succeeded: Blastn
[2023-06-04 21:56:25,967] [INFO] Selected 10 target genomes.
[2023-06-04 21:56:25,968] [INFO] Target genome list was writen to GCA_902517275.1_AG-325-O10_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 21:56:25,977] [INFO] Task started: fastANI
[2023-06-04 21:56:25,978] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b517e3-3c16-4985-bd06-1c6d76f7b36f/GCA_902517275.1_AG-325-O10_genomic.fna.gz --refList GCA_902517275.1_AG-325-O10_genomic.fna/target_genomes_gtdb.txt --output GCA_902517275.1_AG-325-O10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 21:56:29,240] [INFO] Task succeeded: fastANI
[2023-06-04 21:56:29,255] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 21:56:29,256] [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_902517275.1	s__AAA536-G10 sp902517275	100.0	351	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003278095.1	s__AAA536-G10 sp003278095	94.935	319	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_003282145.1	s__AAA536-G10 sp003282145	93.8709	299	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902528415.1	s__AAA536-G10 sp902528415	93.7672	223	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.26	95.26	0.64	0.64	2	-
GCA_003282435.1	s__AAA536-G10 sp003282435	93.6152	192	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514865.1	s__AAA536-G10 sp902514865	91.8277	142	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	91.5417	267	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622875.1	s__AAA536-G10 sp902622875	89.9078	266	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000421325.1	s__AAA536-G10 sp000421325	86.0767	256	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625215.1	s__AAA536-G10 sp902625215	77.6404	153	355	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 21:56:29,259] [INFO] GTDB search result was written to GCA_902517275.1_AG-325-O10_genomic.fna/result_gtdb.tsv
[2023-06-04 21:56:29,260] [INFO] ===== GTDB Search completed =====
[2023-06-04 21:56:29,264] [INFO] DFAST_QC result json was written to GCA_902517275.1_AG-325-O10_genomic.fna/dqc_result.json
[2023-06-04 21:56:29,265] [INFO] DFAST_QC completed!
[2023-06-04 21:56:29,265] [INFO] Total running time: 0h0m23s