[2024-01-25 20:17:20,747] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:20,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:20,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference
[2024-01-25 20:17:21,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:21,994] [INFO] Task started: Prodigal
[2024-01-25 20:17:21,994] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeadfd58-0f84-4c8d-9c08-10439a3c6ba1/GCF_016881065.1_ASM1688106v1_genomic.fna.gz | prodigal -d GCF_016881065.1_ASM1688106v1_genomic.fna/cds.fna -a GCF_016881065.1_ASM1688106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:31,262] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:31,263] [INFO] Task started: HMMsearch
[2024-01-25 20:17:31,263] [INFO] Running command: hmmsearch --tblout GCF_016881065.1_ASM1688106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference/reference_markers.hmm GCF_016881065.1_ASM1688106v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:31,484] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:31,485] [INFO] Found 6/6 markers.
[2024-01-25 20:17:31,512] [INFO] Query marker FASTA was written to GCF_016881065.1_ASM1688106v1_genomic.fna/markers.fasta
[2024-01-25 20:17:31,512] [INFO] Task started: Blastn
[2024-01-25 20:17:31,512] [INFO] Running command: blastn -query GCF_016881065.1_ASM1688106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference/reference_markers.fasta -out GCF_016881065.1_ASM1688106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:32,059] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:32,061] [INFO] Selected 11 target genomes.
[2024-01-25 20:17:32,062] [INFO] Target genome list was writen to GCF_016881065.1_ASM1688106v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:32,073] [INFO] Task started: fastANI
[2024-01-25 20:17:32,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeadfd58-0f84-4c8d-9c08-10439a3c6ba1/GCF_016881065.1_ASM1688106v1_genomic.fna.gz --refList GCF_016881065.1_ASM1688106v1_genomic.fna/target_genomes.txt --output GCF_016881065.1_ASM1688106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:40,454] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:40,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:40,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:40,462] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:40,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:40,463] [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
Planococcus soli	strain=c23	GCA_016881065.1	2666072	2666072	type	True	100.0	1272	1273	95	conclusive
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	83.6811	867	1273	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_001687565.2	161360	161360	type	True	83.6657	884	1273	95	below_threshold
Planococcus wigleyi	strain=Sa1BUA13	GCA_014836985.1	2762216	2762216	type	True	82.6828	862	1273	95	below_threshold
Planococcus faecalis	strain=AJ003	GCA_002009235.1	1598147	1598147	suspected-type	True	81.1063	680	1273	95	below_threshold
Planococcus halocryophilus	strain=DSM 24743	GCA_001687585.2	1215089	1215089	type	True	80.9047	622	1273	95	below_threshold
Planococcus donghaensis	strain=DSM 22276	GCA_001687665.2	414778	414778	type	True	80.7417	612	1273	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	78.9952	406	1273	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	78.9842	406	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:40,465] [INFO] DFAST Taxonomy check result was written to GCF_016881065.1_ASM1688106v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:40,465] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:40,465] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:40,465] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference/checkm_data
[2024-01-25 20:17:40,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:40,507] [INFO] Task started: CheckM
[2024-01-25 20:17:40,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016881065.1_ASM1688106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016881065.1_ASM1688106v1_genomic.fna/checkm_input GCF_016881065.1_ASM1688106v1_genomic.fna/checkm_result
[2024-01-25 20:18:10,947] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:10,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:10,965] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:10,966] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:10,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016881065.1_ASM1688106v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:10,967] [INFO] Task started: Blastn
[2024-01-25 20:18:10,967] [INFO] Running command: blastn -query GCF_016881065.1_ASM1688106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg937aed0c-cd37-48db-b1f4-3795a467d8c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016881065.1_ASM1688106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:11,767] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:11,773] [INFO] Selected 5 target genomes.
[2024-01-25 20:18:11,773] [INFO] Target genome list was writen to GCF_016881065.1_ASM1688106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:11,777] [INFO] Task started: fastANI
[2024-01-25 20:18:11,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeadfd58-0f84-4c8d-9c08-10439a3c6ba1/GCF_016881065.1_ASM1688106v1_genomic.fna.gz --refList GCF_016881065.1_ASM1688106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016881065.1_ASM1688106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:16,827] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:16,832] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:16,832] [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_016881065.1	s__Planococcus soli	100.0	1272	1273	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018613575.1	s__Planococcus sp018613575	85.6315	919	1273	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687565.2	s__Planococcus antarcticus	83.673	883	1273	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.42	99.42	0.95	0.95	2	-
GCF_007859295.1	s__Planococcus sp007859295	83.2924	888	1273	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836985.1	s__Planococcus sp014836985	82.6889	861	1273	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.16	97.16	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:16,833] [INFO] GTDB search result was written to GCF_016881065.1_ASM1688106v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:16,834] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:16,837] [INFO] DFAST_QC result json was written to GCF_016881065.1_ASM1688106v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:16,837] [INFO] DFAST_QC completed!
[2024-01-25 20:18:16,837] [INFO] Total running time: 0h0m56s