[2024-01-24 14:46:35,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference
[2024-01-24 14:46:37,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,181] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,181] [INFO] Running command: gunzip -c /var/lib/cwl/stg479a3b65-a174-4685-9746-5967c7af0ce0/GCF_001856085.1_ASM185608v1_genomic.fna.gz | prodigal -d GCF_001856085.1_ASM185608v1_genomic.fna/cds.fna -a GCF_001856085.1_ASM185608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:39,653] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:39,653] [INFO] Task started: HMMsearch
[2024-01-24 14:46:39,653] [INFO] Running command: hmmsearch --tblout GCF_001856085.1_ASM185608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference/reference_markers.hmm GCF_001856085.1_ASM185608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:39,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:39,903] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg479a3b65-a174-4685-9746-5967c7af0ce0/GCF_001856085.1_ASM185608v1_genomic.fna.gz]
[2024-01-24 14:46:39,917] [INFO] Query marker FASTA was written to GCF_001856085.1_ASM185608v1_genomic.fna/markers.fasta
[2024-01-24 14:46:39,919] [INFO] Task started: Blastn
[2024-01-24 14:46:39,919] [INFO] Running command: blastn -query GCF_001856085.1_ASM185608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference/reference_markers.fasta -out GCF_001856085.1_ASM185608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:42,351] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:42,354] [INFO] Selected 10 target genomes.
[2024-01-24 14:46:42,354] [INFO] Target genome list was writen to GCF_001856085.1_ASM185608v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:42,433] [INFO] Task started: fastANI
[2024-01-24 14:46:42,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg479a3b65-a174-4685-9746-5967c7af0ce0/GCF_001856085.1_ASM185608v1_genomic.fna.gz --refList GCF_001856085.1_ASM185608v1_genomic.fna/target_genomes.txt --output GCF_001856085.1_ASM185608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:46:47,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:46:47,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:46:47,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:46:47,617] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:46:47,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:46:47,617] [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 salinarum	strain=DSM 23820	GCA_001856085.1	622695	622695	type	True	100.0	278	284	95	conclusive
Planococcus salinarum	strain=ISL-16	GCA_003428865.1	622695	622695	type	True	99.4286	266	284	95	conclusive
Planococcus salinarum	strain=KCTC 13584	GCA_007004625.1	622695	622695	type	True	99.423	267	284	95	conclusive
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	78.9997	108	284	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	78.9106	109	284	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.6875	92	284	95	below_threshold
Planococcus antarcticus	strain=DSM 14505	GCA_000264415.1	161360	161360	type	True	78.6168	87	284	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	77.8415	84	284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:46:47,619] [INFO] DFAST Taxonomy check result was written to GCF_001856085.1_ASM185608v1_genomic.fna/tc_result.tsv
[2024-01-24 14:46:47,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:46:47,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:46:47,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference/checkm_data
[2024-01-24 14:46:47,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:46:47,633] [INFO] Task started: CheckM
[2024-01-24 14:46:47,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001856085.1_ASM185608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001856085.1_ASM185608v1_genomic.fna/checkm_input GCF_001856085.1_ASM185608v1_genomic.fna/checkm_result
[2024-01-24 14:47:06,207] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:06,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:06,233] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:06,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:06,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001856085.1_ASM185608v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:06,234] [INFO] Task started: Blastn
[2024-01-24 14:47:06,234] [INFO] Running command: blastn -query GCF_001856085.1_ASM185608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f485d91-c361-426b-85e2-74bcc446d251/dqc_reference/reference_markers_gtdb.fasta -out GCF_001856085.1_ASM185608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:06,701] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:06,704] [INFO] Selected 8 target genomes.
[2024-01-24 14:47:06,704] [INFO] Target genome list was writen to GCF_001856085.1_ASM185608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:06,712] [INFO] Task started: fastANI
[2024-01-24 14:47:06,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg479a3b65-a174-4685-9746-5967c7af0ce0/GCF_001856085.1_ASM185608v1_genomic.fna.gz --refList GCF_001856085.1_ASM185608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001856085.1_ASM185608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:11,170] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:11,178] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:11,178] [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_007004625.1	s__Planococcus salinarum	99.4348	267	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003289955.1	s__Planococcus halotolerans	82.7736	214	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.14	99.14	0.94	0.94	2	-
GCF_003668635.1	s__Planococcus sp003668635	82.7304	206	284	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_003428875.1	s__Planococcus okeanokoites	82.5331	194	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.50	97.25	0.88	0.87	3	-
GCF_017873465.1	s__Planococcus mcmeekinii	82.1678	192	284	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_000775575.1	s__Planococcus sp000775575	81.0333	148	284	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_018613655.1	s__Planococcus sp018613655	78.8993	90	284	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_003289925.1	s__Planococcus maitriensis	77.8415	84	284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:11,180] [INFO] GTDB search result was written to GCF_001856085.1_ASM185608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:11,181] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:11,183] [INFO] DFAST_QC result json was written to GCF_001856085.1_ASM185608v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:11,184] [INFO] DFAST_QC completed!
[2024-01-24 14:47:11,184] [INFO] Total running time: 0h0m36s