[2024-01-24 13:46:01,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference
[2024-01-24 13:46:02,932] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,932] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,933] [INFO] Running command: gunzip -c /var/lib/cwl/stg89b79174-660c-4ea6-837f-a6faaaec9e42/GCF_013425485.1_ASM1342548v1_genomic.fna.gz | prodigal -d GCF_013425485.1_ASM1342548v1_genomic.fna/cds.fna -a GCF_013425485.1_ASM1342548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,057] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,058] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,058] [INFO] Running command: hmmsearch --tblout GCF_013425485.1_ASM1342548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference/reference_markers.hmm GCF_013425485.1_ASM1342548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:17,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:17,436] [INFO] Found 6/6 markers.
[2024-01-24 13:46:17,495] [INFO] Query marker FASTA was written to GCF_013425485.1_ASM1342548v1_genomic.fna/markers.fasta
[2024-01-24 13:46:17,496] [INFO] Task started: Blastn
[2024-01-24 13:46:17,496] [INFO] Running command: blastn -query GCF_013425485.1_ASM1342548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference/reference_markers.fasta -out GCF_013425485.1_ASM1342548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:18,194] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:18,198] [INFO] Selected 27 target genomes.
[2024-01-24 13:46:18,198] [INFO] Target genome list was writen to GCF_013425485.1_ASM1342548v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:18,218] [INFO] Task started: fastANI
[2024-01-24 13:46:18,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b79174-660c-4ea6-837f-a6faaaec9e42/GCF_013425485.1_ASM1342548v1_genomic.fna.gz --refList GCF_013425485.1_ASM1342548v1_genomic.fna/target_genomes.txt --output GCF_013425485.1_ASM1342548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:37,032] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:37,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:37,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:37,038] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:37,038] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:37,038] [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	81.9862	1269	2059	95	below_threshold
Zooshikella ganghwensis	strain=DSM 15267	GCA_000428585.1	202772	202772	type	True	77.3005	125	2059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:37,039] [INFO] DFAST Taxonomy check result was written to GCF_013425485.1_ASM1342548v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:37,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:37,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:37,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference/checkm_data
[2024-01-24 13:46:37,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:37,106] [INFO] Task started: CheckM
[2024-01-24 13:46:37,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013425485.1_ASM1342548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013425485.1_ASM1342548v1_genomic.fna/checkm_input GCF_013425485.1_ASM1342548v1_genomic.fna/checkm_result
[2024-01-24 13:47:24,212] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:24,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:24,232] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:24,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:24,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013425485.1_ASM1342548v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:24,234] [INFO] Task started: Blastn
[2024-01-24 13:47:24,234] [INFO] Running command: blastn -query GCF_013425485.1_ASM1342548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96c0baa6-5031-434e-a000-6e13965c4b35/dqc_reference/reference_markers_gtdb.fasta -out GCF_013425485.1_ASM1342548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:25,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:25,236] [INFO] Selected 21 target genomes.
[2024-01-24 13:47:25,236] [INFO] Target genome list was writen to GCF_013425485.1_ASM1342548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:25,252] [INFO] Task started: fastANI
[2024-01-24 13:47:25,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg89b79174-660c-4ea6-837f-a6faaaec9e42/GCF_013425485.1_ASM1342548v1_genomic.fna.gz --refList GCF_013425485.1_ASM1342548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013425485.1_ASM1342548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:41,826] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:41,835] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:41,836] [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	100.0	2049	2059	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	81.9749	1273	2059	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	77.3509	122	2059	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	76.8617	121	2059	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 13:47:41,838] [INFO] GTDB search result was written to GCF_013425485.1_ASM1342548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:41,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:41,840] [INFO] DFAST_QC result json was written to GCF_013425485.1_ASM1342548v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:41,841] [INFO] DFAST_QC completed!
[2024-01-24 13:47:41,841] [INFO] Total running time: 0h1m40s