[2023-06-19 12:58:14,907] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:58:14,909] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:58:14,910] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference
[2023-06-19 12:58:16,204] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:58:16,205] [INFO] Task started: Prodigal
[2023-06-19 12:58:16,206] [INFO] Running command: gunzip -c /var/lib/cwl/stg572b5ae5-47d4-4a9d-b184-c6d119103ed0/GCA_018660785.1_ASM1866078v1_genomic.fna.gz | prodigal -d GCA_018660785.1_ASM1866078v1_genomic.fna/cds.fna -a GCA_018660785.1_ASM1866078v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:58:21,118] [INFO] Task succeeded: Prodigal
[2023-06-19 12:58:21,119] [INFO] Task started: HMMsearch
[2023-06-19 12:58:21,119] [INFO] Running command: hmmsearch --tblout GCA_018660785.1_ASM1866078v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference/reference_markers.hmm GCA_018660785.1_ASM1866078v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:58:21,351] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:58:21,352] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg572b5ae5-47d4-4a9d-b184-c6d119103ed0/GCA_018660785.1_ASM1866078v1_genomic.fna.gz]
[2023-06-19 12:58:21,374] [INFO] Query marker FASTA was written to GCA_018660785.1_ASM1866078v1_genomic.fna/markers.fasta
[2023-06-19 12:58:21,375] [INFO] Task started: Blastn
[2023-06-19 12:58:21,375] [INFO] Running command: blastn -query GCA_018660785.1_ASM1866078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference/reference_markers.fasta -out GCA_018660785.1_ASM1866078v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:58:22,003] [INFO] Task succeeded: Blastn
[2023-06-19 12:58:22,023] [INFO] Selected 28 target genomes.
[2023-06-19 12:58:22,023] [INFO] Target genome list was writen to GCA_018660785.1_ASM1866078v1_genomic.fna/target_genomes.txt
[2023-06-19 12:58:22,025] [INFO] Task started: fastANI
[2023-06-19 12:58:22,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg572b5ae5-47d4-4a9d-b184-c6d119103ed0/GCA_018660785.1_ASM1866078v1_genomic.fna.gz --refList GCA_018660785.1_ASM1866078v1_genomic.fna/target_genomes.txt --output GCA_018660785.1_ASM1866078v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:58:38,582] [INFO] Task succeeded: fastANI
[2023-06-19 12:58:38,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:58:38,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:58:38,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:58:38,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:58:38,586] [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 12:58:38,589] [INFO] DFAST Taxonomy check result was written to GCA_018660785.1_ASM1866078v1_genomic.fna/tc_result.tsv
[2023-06-19 12:58:38,589] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:58:38,590] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:58:38,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference/checkm_data
[2023-06-19 12:58:38,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:58:38,629] [INFO] Task started: CheckM
[2023-06-19 12:58:38,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018660785.1_ASM1866078v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018660785.1_ASM1866078v1_genomic.fna/checkm_input GCA_018660785.1_ASM1866078v1_genomic.fna/checkm_result
[2023-06-19 12:59:00,586] [INFO] Task succeeded: CheckM
[2023-06-19 12:59:00,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:59:00,608] [INFO] ===== Completeness check finished =====
[2023-06-19 12:59:00,608] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:59:00,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018660785.1_ASM1866078v1_genomic.fna/markers.fasta)
[2023-06-19 12:59:00,609] [INFO] Task started: Blastn
[2023-06-19 12:59:00,609] [INFO] Running command: blastn -query GCA_018660785.1_ASM1866078v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e37b9a1-5e19-42e4-8943-2b64a7ed1fc9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018660785.1_ASM1866078v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:59:01,594] [INFO] Task succeeded: Blastn
[2023-06-19 12:59:01,599] [INFO] Selected 24 target genomes.
[2023-06-19 12:59:01,599] [INFO] Target genome list was writen to GCA_018660785.1_ASM1866078v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:59:01,603] [INFO] Task started: fastANI
[2023-06-19 12:59:01,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg572b5ae5-47d4-4a9d-b184-c6d119103ed0/GCA_018660785.1_ASM1866078v1_genomic.fna.gz --refList GCA_018660785.1_ASM1866078v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018660785.1_ASM1866078v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:59:12,175] [INFO] Task succeeded: fastANI
[2023-06-19 12:59:12,189] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:59:12,189] [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	99.2095	451	546	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	94.5834	488	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.01	96.90	0.92	0.88	5	-
GCA_009937065.1	s__Luminiphilus sp009937065	77.9444	96	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227505.4	s__Luminiphilus sp000227505	77.1921	80	546	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	77.1486	76	546	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	77.1174	106	546	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	77.075	64	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	100.00	100.00	0.97	0.97	2	-
GCA_002862405.1	s__Luminiphilus sp002862405	76.6871	87	546	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	76.6698	55	546	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:59:12,191] [INFO] GTDB search result was written to GCA_018660785.1_ASM1866078v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:59:12,192] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:59:12,194] [INFO] DFAST_QC result json was written to GCA_018660785.1_ASM1866078v1_genomic.fna/dqc_result.json
[2023-06-19 12:59:12,194] [INFO] DFAST_QC completed!
[2023-06-19 12:59:12,194] [INFO] Total running time: 0h0m57s