[2024-01-24 12:53:54,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:54,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:54,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference
[2024-01-24 12:53:55,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:55,768] [INFO] Task started: Prodigal
[2024-01-24 12:53:55,768] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb57f73d-5f70-4d6c-86ea-d678ed8ced0d/GCF_011009015.1_ASM1100901v1_genomic.fna.gz | prodigal -d GCF_011009015.1_ASM1100901v1_genomic.fna/cds.fna -a GCF_011009015.1_ASM1100901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:09,930] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:09,930] [INFO] Task started: HMMsearch
[2024-01-24 12:54:09,930] [INFO] Running command: hmmsearch --tblout GCF_011009015.1_ASM1100901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference/reference_markers.hmm GCF_011009015.1_ASM1100901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:10,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:10,274] [INFO] Found 6/6 markers.
[2024-01-24 12:54:10,350] [INFO] Query marker FASTA was written to GCF_011009015.1_ASM1100901v1_genomic.fna/markers.fasta
[2024-01-24 12:54:10,351] [INFO] Task started: Blastn
[2024-01-24 12:54:10,351] [INFO] Running command: blastn -query GCF_011009015.1_ASM1100901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference/reference_markers.fasta -out GCF_011009015.1_ASM1100901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:11,028] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:11,032] [INFO] Selected 28 target genomes.
[2024-01-24 12:54:11,032] [INFO] Target genome list was writen to GCF_011009015.1_ASM1100901v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:11,044] [INFO] Task started: fastANI
[2024-01-24 12:54:11,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb57f73d-5f70-4d6c-86ea-d678ed8ced0d/GCF_011009015.1_ASM1100901v1_genomic.fna.gz --refList GCF_011009015.1_ASM1100901v1_genomic.fna/target_genomes.txt --output GCF_011009015.1_ASM1100901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:34,119] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:34,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:34,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:34,124] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:34,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:34,124] [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	100.0	2226	2228	95	conclusive
Zooshikella ganghwensis	strain=DSM 15267	GCA_000428585.1	202772	202772	type	True	77.3592	127	2228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:34,125] [INFO] DFAST Taxonomy check result was written to GCF_011009015.1_ASM1100901v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:34,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:34,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:34,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference/checkm_data
[2024-01-24 12:54:34,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:34,189] [INFO] Task started: CheckM
[2024-01-24 12:54:34,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011009015.1_ASM1100901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011009015.1_ASM1100901v1_genomic.fna/checkm_input GCF_011009015.1_ASM1100901v1_genomic.fna/checkm_result
[2024-01-24 12:55:18,161] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:18,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:18,182] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:18,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:18,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011009015.1_ASM1100901v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:18,184] [INFO] Task started: Blastn
[2024-01-24 12:55:18,184] [INFO] Running command: blastn -query GCF_011009015.1_ASM1100901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07559eeb-24c4-4325-9dd2-6a03defaa691/dqc_reference/reference_markers_gtdb.fasta -out GCF_011009015.1_ASM1100901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:19,191] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:19,195] [INFO] Selected 19 target genomes.
[2024-01-24 12:55:19,195] [INFO] Target genome list was writen to GCF_011009015.1_ASM1100901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:19,207] [INFO] Task started: fastANI
[2024-01-24 12:55:19,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb57f73d-5f70-4d6c-86ea-d678ed8ced0d/GCF_011009015.1_ASM1100901v1_genomic.fna.gz --refList GCF_011009015.1_ASM1100901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011009015.1_ASM1100901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:35,093] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:35,098] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:35,099] [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_011009015.1	s__Spartinivicinus ruber	100.0	2225	2228	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_013425485.1	s__Spartinivicinus sp013425485	81.9705	1273	2228	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	77.3964	126	2228	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	77.0552	143	2228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Zooshikellaceae;g__Zooshikella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:35,100] [INFO] GTDB search result was written to GCF_011009015.1_ASM1100901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:35,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:35,103] [INFO] DFAST_QC result json was written to GCF_011009015.1_ASM1100901v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:35,103] [INFO] DFAST_QC completed!
[2024-01-24 12:55:35,103] [INFO] Total running time: 0h1m41s