[2024-01-24 14:07:31,020] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,023] [INFO] DQC Reference Directory: /var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference
[2024-01-24 14:07:32,263] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,264] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,265] [INFO] Running command: gunzip -c /var/lib/cwl/stga6cd2987-470e-4255-88ca-98dfac409eac/GCF_007004765.1_ASM700476v1_genomic.fna.gz | prodigal -d GCF_007004765.1_ASM700476v1_genomic.fna/cds.fna -a GCF_007004765.1_ASM700476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:44,083] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:44,084] [INFO] Task started: HMMsearch
[2024-01-24 14:07:44,084] [INFO] Running command: hmmsearch --tblout GCF_007004765.1_ASM700476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference/reference_markers.hmm GCF_007004765.1_ASM700476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:44,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:44,442] [INFO] Found 6/6 markers.
[2024-01-24 14:07:44,496] [INFO] Query marker FASTA was written to GCF_007004765.1_ASM700476v1_genomic.fna/markers.fasta
[2024-01-24 14:07:44,497] [INFO] Task started: Blastn
[2024-01-24 14:07:44,497] [INFO] Running command: blastn -query GCF_007004765.1_ASM700476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference/reference_markers.fasta -out GCF_007004765.1_ASM700476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:45,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:45,222] [INFO] Selected 29 target genomes.
[2024-01-24 14:07:45,223] [INFO] Target genome list was writen to GCF_007004765.1_ASM700476v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:45,239] [INFO] Task started: fastANI
[2024-01-24 14:07:45,240] [INFO] Running command: fastANI --query /var/lib/cwl/stga6cd2987-470e-4255-88ca-98dfac409eac/GCF_007004765.1_ASM700476v1_genomic.fna.gz --refList GCF_007004765.1_ASM700476v1_genomic.fna/target_genomes.txt --output GCF_007004765.1_ASM700476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:08:03,961] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:03,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:08:03,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:08:03,967] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:08:03,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:08:03,967] [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
Aliikangiella marina	strain=GYP-15	GCA_007004765.1	1712262	1712262	type	True	100.0	1760	1773	95	conclusive
Aliikangiella coralliicola	strain=M105	GCA_007004725.1	2592383	2592383	type	True	77.6645	132	1773	95	below_threshold
Pleionea sediminis	strain=S1-5-21	GCA_007570825.1	2569479	2569479	type	True	75.9698	53	1773	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:08:03,969] [INFO] DFAST Taxonomy check result was written to GCF_007004765.1_ASM700476v1_genomic.fna/tc_result.tsv
[2024-01-24 14:08:03,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:08:03,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:08:03,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference/checkm_data
[2024-01-24 14:08:03,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:08:04,026] [INFO] Task started: CheckM
[2024-01-24 14:08:04,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004765.1_ASM700476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004765.1_ASM700476v1_genomic.fna/checkm_input GCF_007004765.1_ASM700476v1_genomic.fna/checkm_result
[2024-01-24 14:08:45,107] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:45,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:45,131] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:45,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:45,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004765.1_ASM700476v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:45,132] [INFO] Task started: Blastn
[2024-01-24 14:08:45,132] [INFO] Running command: blastn -query GCF_007004765.1_ASM700476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c12d8b-3ace-4655-a723-0f878075906c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004765.1_ASM700476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:46,254] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:46,259] [INFO] Selected 24 target genomes.
[2024-01-24 14:08:46,259] [INFO] Target genome list was writen to GCF_007004765.1_ASM700476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:46,278] [INFO] Task started: fastANI
[2024-01-24 14:08:46,278] [INFO] Running command: fastANI --query /var/lib/cwl/stga6cd2987-470e-4255-88ca-98dfac409eac/GCF_007004765.1_ASM700476v1_genomic.fna.gz --refList GCF_007004765.1_ASM700476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004765.1_ASM700476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:01,639] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:01,648] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:01,649] [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_007004765.1	s__Aliikangiella marina	100.0	1760	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Aliikangiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015687155.1	s__Aliikangiella sp015687155	78.2302	100	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Aliikangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004725.1	s__Aliikangiella coralliicola	77.671	131	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Aliikangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479925.1	s__GCA-002733465 sp905479925	76.7186	66	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__GCA-002733465	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570825.1	s__Pleionea sediminis	75.9564	52	1773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Pleionea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:01,650] [INFO] GTDB search result was written to GCF_007004765.1_ASM700476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:01,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:01,654] [INFO] DFAST_QC result json was written to GCF_007004765.1_ASM700476v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:01,655] [INFO] DFAST_QC completed!
[2024-01-24 14:09:01,655] [INFO] Total running time: 0h1m31s