[2024-01-24 13:12:56,062] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,065] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,065] [INFO] DQC Reference Directory: /var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference
[2024-01-24 13:12:57,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,480] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg9238112d-5ad3-402e-9945-43b463128dd3/GCF_004761885.1_ASM476188v1_genomic.fna.gz | prodigal -d GCF_004761885.1_ASM476188v1_genomic.fna/cds.fna -a GCF_004761885.1_ASM476188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:07,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:07,151] [INFO] Task started: HMMsearch
[2024-01-24 13:13:07,151] [INFO] Running command: hmmsearch --tblout GCF_004761885.1_ASM476188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference/reference_markers.hmm GCF_004761885.1_ASM476188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:07,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:07,440] [INFO] Found 6/6 markers.
[2024-01-24 13:13:07,469] [INFO] Query marker FASTA was written to GCF_004761885.1_ASM476188v1_genomic.fna/markers.fasta
[2024-01-24 13:13:07,470] [INFO] Task started: Blastn
[2024-01-24 13:13:07,470] [INFO] Running command: blastn -query GCF_004761885.1_ASM476188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference/reference_markers.fasta -out GCF_004761885.1_ASM476188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:08,062] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:08,065] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:08,065] [INFO] Target genome list was writen to GCF_004761885.1_ASM476188v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:08,080] [INFO] Task started: fastANI
[2024-01-24 13:13:08,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg9238112d-5ad3-402e-9945-43b463128dd3/GCF_004761885.1_ASM476188v1_genomic.fna.gz --refList GCF_004761885.1_ASM476188v1_genomic.fna/target_genomes.txt --output GCF_004761885.1_ASM476188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:16,815] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:16,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:16,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:16,824] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:16,824] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:16,824] [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 citreus	strain=DSM 20549	GCA_004761885.1	1373	1373	type	True	100.0	1075	1079	95	conclusive
Planococcus citreus	strain=DSM 20549	GCA_003664125.1	1373	1373	type	True	99.9838	1076	1079	95	conclusive
Planococcus rifietoensis	strain=M8	GCA_001465795.2	200991	200991	type	True	92.9906	963	1079	95	below_threshold
Planococcus maitriensis	strain=S1	GCA_003289925.1	221799	221799	type	True	90.1055	894	1079	95	below_threshold
Planococcus plakortidis	strain=DSM 23997	GCA_001687605.2	1038856	1038856	type	True	88.3974	918	1079	95	below_threshold
Planococcus maritimus	strain=DSM 17275	GCA_001687625.2	192421	192421	type	True	85.6747	869	1079	95	below_threshold
Planococcus koreensis	strain=10704	GCA_004761975.1	112331	112331	type	True	78.5824	333	1079	95	below_threshold
Planococcus koreensis	strain=DSM 15895	GCA_014202615.1	112331	112331	type	True	78.5153	336	1079	95	below_threshold
Planococcus ruber	strain=CGMCC 1.19134	GCA_022819085.1	2027871	2027871	type	True	78.2318	282	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:16,826] [INFO] DFAST Taxonomy check result was written to GCF_004761885.1_ASM476188v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:16,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:16,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:16,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference/checkm_data
[2024-01-24 13:13:16,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:16,860] [INFO] Task started: CheckM
[2024-01-24 13:13:16,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004761885.1_ASM476188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004761885.1_ASM476188v1_genomic.fna/checkm_input GCF_004761885.1_ASM476188v1_genomic.fna/checkm_result
[2024-01-24 13:13:50,578] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:50,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:50,592] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:50,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:50,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004761885.1_ASM476188v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:50,593] [INFO] Task started: Blastn
[2024-01-24 13:13:50,593] [INFO] Running command: blastn -query GCF_004761885.1_ASM476188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec8034be-7a47-4d7d-9bcb-ed728c1cbb2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004761885.1_ASM476188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:51,423] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:51,427] [INFO] Selected 7 target genomes.
[2024-01-24 13:13:51,427] [INFO] Target genome list was writen to GCF_004761885.1_ASM476188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:51,440] [INFO] Task started: fastANI
[2024-01-24 13:13:51,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg9238112d-5ad3-402e-9945-43b463128dd3/GCF_004761885.1_ASM476188v1_genomic.fna.gz --refList GCF_004761885.1_ASM476188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004761885.1_ASM476188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:58,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:58,127] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:58,128] [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_003664125.1	s__Planococcus citreus	99.9838	1076	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_001465795.2	s__Planococcus rifietoensis	92.9906	963	1079	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_002833405.1	s__Planococcus sp002833405	92.3578	947	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.89	99.88	0.99	0.97	4	-
GCF_018283455.1	s__Planococcus sp018283455	91.0492	947	1079	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	90.0909	895	1079	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_019042655.1	s__Planococcus sp019042655	89.531	906	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001592825.1	s__Planococcus maritimus_C	85.7144	852	1079	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Planococcus	95.0	97.02	95.52	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:58,129] [INFO] GTDB search result was written to GCF_004761885.1_ASM476188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:58,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:58,132] [INFO] DFAST_QC result json was written to GCF_004761885.1_ASM476188v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:58,132] [INFO] DFAST_QC completed!
[2024-01-24 13:13:58,132] [INFO] Total running time: 0h1m2s