[2024-01-24 15:26:39,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference
[2024-01-24 15:26:41,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,055] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,055] [INFO] Running command: gunzip -c /var/lib/cwl/stgf237601b-273d-43e2-a556-825424538ae5/GCF_009650135.1_ASM965013v1_genomic.fna.gz | prodigal -d GCF_009650135.1_ASM965013v1_genomic.fna/cds.fna -a GCF_009650135.1_ASM965013v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:48,621] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:48,622] [INFO] Task started: HMMsearch
[2024-01-24 15:26:48,622] [INFO] Running command: hmmsearch --tblout GCF_009650135.1_ASM965013v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference/reference_markers.hmm GCF_009650135.1_ASM965013v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:48,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:48,852] [INFO] Found 6/6 markers.
[2024-01-24 15:26:48,878] [INFO] Query marker FASTA was written to GCF_009650135.1_ASM965013v1_genomic.fna/markers.fasta
[2024-01-24 15:26:48,878] [INFO] Task started: Blastn
[2024-01-24 15:26:48,878] [INFO] Running command: blastn -query GCF_009650135.1_ASM965013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference/reference_markers.fasta -out GCF_009650135.1_ASM965013v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:49,655] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:49,659] [INFO] Selected 29 target genomes.
[2024-01-24 15:26:49,659] [INFO] Target genome list was writen to GCF_009650135.1_ASM965013v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:49,683] [INFO] Task started: fastANI
[2024-01-24 15:26:49,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgf237601b-273d-43e2-a556-825424538ae5/GCF_009650135.1_ASM965013v1_genomic.fna.gz --refList GCF_009650135.1_ASM965013v1_genomic.fna/target_genomes.txt --output GCF_009650135.1_ASM965013v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:08,117] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:08,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:08,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:08,124] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:08,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:08,124] [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
Litoricola lipolytica	strain=IMCC 1097	GCA_009650135.1	418701	418701	type	True	100.0	780	782	95	conclusive
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	76.6895	59	782	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.2345	53	782	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.018	51	782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:08,125] [INFO] DFAST Taxonomy check result was written to GCF_009650135.1_ASM965013v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:08,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:08,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:08,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference/checkm_data
[2024-01-24 15:27:08,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,152] [INFO] Task started: CheckM
[2024-01-24 15:27:08,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009650135.1_ASM965013v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009650135.1_ASM965013v1_genomic.fna/checkm_input GCF_009650135.1_ASM965013v1_genomic.fna/checkm_result
[2024-01-24 15:27:36,386] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:36,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,407] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:36,407] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:36,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009650135.1_ASM965013v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:36,408] [INFO] Task started: Blastn
[2024-01-24 15:27:36,408] [INFO] Running command: blastn -query GCF_009650135.1_ASM965013v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8bf6e88-f2d4-4a59-90ab-8dd80d041277/dqc_reference/reference_markers_gtdb.fasta -out GCF_009650135.1_ASM965013v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:37,620] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:37,625] [INFO] Selected 28 target genomes.
[2024-01-24 15:27:37,625] [INFO] Target genome list was writen to GCF_009650135.1_ASM965013v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:37,647] [INFO] Task started: fastANI
[2024-01-24 15:27:37,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgf237601b-273d-43e2-a556-825424538ae5/GCF_009650135.1_ASM965013v1_genomic.fna.gz --refList GCF_009650135.1_ASM965013v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009650135.1_ASM965013v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:57,531] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:57,545] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:57,545] [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_009650135.1	s__Litoricola lipolytica	100.0	780	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__Litoricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012269655.1	s__Litoricola sp012269655	77.7331	85	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__Litoricola	95.0	98.73	98.73	0.83	0.83	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.3126	51	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282475.1	s__Pseudomonas_E sp000282475	75.449	54	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_013373935.1	s__Pseudomonas_E sp002438125	75.018	51	782	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:57,547] [INFO] GTDB search result was written to GCF_009650135.1_ASM965013v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:57,547] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:57,550] [INFO] DFAST_QC result json was written to GCF_009650135.1_ASM965013v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:57,550] [INFO] DFAST_QC completed!
[2024-01-24 15:27:57,551] [INFO] Total running time: 0h1m18s