[2024-01-25 20:21:20,451] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:20,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:20,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference
[2024-01-25 20:21:21,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:21,543] [INFO] Task started: Prodigal
[2024-01-25 20:21:21,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg18f6451d-2a0f-4c3f-8b88-2aeeb7e3a81f/GCF_026309355.1_ASM2630935v1_genomic.fna.gz | prodigal -d GCF_026309355.1_ASM2630935v1_genomic.fna/cds.fna -a GCF_026309355.1_ASM2630935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:35,158] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:35,158] [INFO] Task started: HMMsearch
[2024-01-25 20:21:35,158] [INFO] Running command: hmmsearch --tblout GCF_026309355.1_ASM2630935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference/reference_markers.hmm GCF_026309355.1_ASM2630935v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:35,486] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:35,487] [INFO] Found 6/6 markers.
[2024-01-25 20:21:35,547] [INFO] Query marker FASTA was written to GCF_026309355.1_ASM2630935v1_genomic.fna/markers.fasta
[2024-01-25 20:21:35,547] [INFO] Task started: Blastn
[2024-01-25 20:21:35,547] [INFO] Running command: blastn -query GCF_026309355.1_ASM2630935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference/reference_markers.fasta -out GCF_026309355.1_ASM2630935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:36,180] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:36,184] [INFO] Selected 27 target genomes.
[2024-01-25 20:21:36,184] [INFO] Target genome list was writen to GCF_026309355.1_ASM2630935v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:36,212] [INFO] Task started: fastANI
[2024-01-25 20:21:36,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg18f6451d-2a0f-4c3f-8b88-2aeeb7e3a81f/GCF_026309355.1_ASM2630935v1_genomic.fna.gz --refList GCF_026309355.1_ASM2630935v1_genomic.fna/target_genomes.txt --output GCF_026309355.1_ASM2630935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:57,563] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:57,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:57,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:57,568] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:21:57,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:21:57,568] [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
Spartinivicinus ruber	strain=S2-4-1H	GCA_011009015.1	2683272	2683272	type	True	82.2231	1344	2290	95	below_threshold
Zooshikella ganghwensis	strain=DSM 15267	GCA_000428585.1	202772	202772	type	True	77.1362	155	2290	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:57,569] [INFO] DFAST Taxonomy check result was written to GCF_026309355.1_ASM2630935v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:57,570] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:57,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:57,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference/checkm_data
[2024-01-25 20:21:57,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:57,636] [INFO] Task started: CheckM
[2024-01-25 20:21:57,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026309355.1_ASM2630935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026309355.1_ASM2630935v1_genomic.fna/checkm_input GCF_026309355.1_ASM2630935v1_genomic.fna/checkm_result
[2024-01-25 20:22:40,638] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:40,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:40,664] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:40,664] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:40,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026309355.1_ASM2630935v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:40,665] [INFO] Task started: Blastn
[2024-01-25 20:22:40,665] [INFO] Running command: blastn -query GCF_026309355.1_ASM2630935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bbde4d1-9be6-461b-877a-8dca72e27180/dqc_reference/reference_markers_gtdb.fasta -out GCF_026309355.1_ASM2630935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:41,615] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:41,618] [INFO] Selected 21 target genomes.
[2024-01-25 20:22:41,618] [INFO] Target genome list was writen to GCF_026309355.1_ASM2630935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:41,648] [INFO] Task started: fastANI
[2024-01-25 20:22:41,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg18f6451d-2a0f-4c3f-8b88-2aeeb7e3a81f/GCF_026309355.1_ASM2630935v1_genomic.fna.gz --refList GCF_026309355.1_ASM2630935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026309355.1_ASM2630935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:59,536] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:59,540] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:59,540] [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_013425485.1	s__Spartinivicinus sp013425485	99.9123	2031	2290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Spartinivicinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011009015.1	s__Spartinivicinus ruber	82.2192	1347	2290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Spartinivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428585.1	s__Zooshikella ganghwensis	77.1969	149	2290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Zooshikella	95.0	97.38	97.05	0.91	0.90	4	-
GCF_018837975.1	s__Zooshikella sp018837975	76.8597	123	2290	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Zooshikella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:59,543] [INFO] GTDB search result was written to GCF_026309355.1_ASM2630935v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:59,543] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:59,545] [INFO] DFAST_QC result json was written to GCF_026309355.1_ASM2630935v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:59,545] [INFO] DFAST_QC completed!
[2024-01-25 20:22:59,545] [INFO] Total running time: 0h1m39s