[2024-01-24 12:05:58,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:58,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:58,935] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference
[2024-01-24 12:06:00,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,327] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,327] [INFO] Running command: gunzip -c /var/lib/cwl/stgc92e0e11-7cc0-4916-9c50-9d867fea2670/GCF_016909185.1_ASM1690918v1_genomic.fna.gz | prodigal -d GCF_016909185.1_ASM1690918v1_genomic.fna/cds.fna -a GCF_016909185.1_ASM1690918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:12,844] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:12,844] [INFO] Task started: HMMsearch
[2024-01-24 12:06:12,844] [INFO] Running command: hmmsearch --tblout GCF_016909185.1_ASM1690918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference/reference_markers.hmm GCF_016909185.1_ASM1690918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:13,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:13,183] [INFO] Found 6/6 markers.
[2024-01-24 12:06:13,223] [INFO] Query marker FASTA was written to GCF_016909185.1_ASM1690918v1_genomic.fna/markers.fasta
[2024-01-24 12:06:13,223] [INFO] Task started: Blastn
[2024-01-24 12:06:13,223] [INFO] Running command: blastn -query GCF_016909185.1_ASM1690918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference/reference_markers.fasta -out GCF_016909185.1_ASM1690918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:13,853] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:13,857] [INFO] Selected 27 target genomes.
[2024-01-24 12:06:13,858] [INFO] Target genome list was writen to GCF_016909185.1_ASM1690918v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:13,870] [INFO] Task started: fastANI
[2024-01-24 12:06:13,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92e0e11-7cc0-4916-9c50-9d867fea2670/GCF_016909185.1_ASM1690918v1_genomic.fna.gz --refList GCF_016909185.1_ASM1690918v1_genomic.fna/target_genomes.txt --output GCF_016909185.1_ASM1690918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:35,294] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:35,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:35,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:35,306] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:35,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:35,307] [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
Siminovitchia thermophila	strain=DSM 105453	GCA_016909185.1	1245522	1245522	type	True	100.0	1527	1533	95	conclusive
Siminovitchia fordii	strain=DSM 16014	GCA_000374565.1	254759	254759	type	True	78.7116	256	1533	95	below_threshold
Siminovitchia fortis	strain=DSM 16012	GCA_003605365.2	254758	254758	type	True	77.807	244	1533	95	below_threshold
Siminovitchia acidinfaciens	strain=3-2-2	GCA_003605385.2	2321395	2321395	type	True	77.102	228	1533	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	76.8325	82	1533	95	below_threshold
Lederbergia wuyishanensis	strain=CGMCC 1.12709	GCA_022900255.1	1347903	1347903	type	True	76.4847	89	1533	95	below_threshold
Lederbergia panacisoli	strain=KACC 17503	GCA_024626525.1	1255251	1255251	type	True	76.2861	90	1533	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	75.8892	66	1533	95	below_threshold
Margalitia shackletonii	strain=LMG 18435	GCA_001420715.1	157838	157838	type	True	75.7352	56	1533	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	75.6978	51	1533	95	below_threshold
Bacillus badius	strain=NBRC 15713	GCA_001591605.1	1455	1455	type	True	75.6178	57	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:35,309] [INFO] DFAST Taxonomy check result was written to GCF_016909185.1_ASM1690918v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:35,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:35,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:35,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference/checkm_data
[2024-01-24 12:06:35,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:35,380] [INFO] Task started: CheckM
[2024-01-24 12:06:35,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016909185.1_ASM1690918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016909185.1_ASM1690918v1_genomic.fna/checkm_input GCF_016909185.1_ASM1690918v1_genomic.fna/checkm_result
[2024-01-24 12:07:15,243] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:15,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:15,262] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:15,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:15,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016909185.1_ASM1690918v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:15,263] [INFO] Task started: Blastn
[2024-01-24 12:07:15,263] [INFO] Running command: blastn -query GCF_016909185.1_ASM1690918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbccea9e-b2c6-4014-a938-cb88ef998eb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016909185.1_ASM1690918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,039] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,046] [INFO] Selected 28 target genomes.
[2024-01-24 12:07:16,046] [INFO] Target genome list was writen to GCF_016909185.1_ASM1690918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:16,064] [INFO] Task started: fastANI
[2024-01-24 12:07:16,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgc92e0e11-7cc0-4916-9c50-9d867fea2670/GCF_016909185.1_ASM1690918v1_genomic.fna.gz --refList GCF_016909185.1_ASM1690918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016909185.1_ASM1690918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:40,311] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:40,322] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:40,322] [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_016909185.1	s__Siminovitchia thermophila	100.0	1527	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	99.46	99.46	0.95	0.95	2	conclusive
GCF_000374565.1	s__Siminovitchia fordii	78.6949	257	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.95	97.34	0.95	0.89	4	-
GCF_009928435.1	s__Siminovitchia sp009928435	77.8874	204	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605365.2	s__Siminovitchia fortis	77.7938	245	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.09	98.04	0.87	0.87	16	-
GCF_008764245.1	s__Lederbergia ruris	77.495	74	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Lederbergia	95.0	98.48	98.48	0.86	0.86	2	-
GCF_018343695.1	s__FJAT-49711 sp018343695	76.8325	82	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__FJAT-49711	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343515.1	s__Bacillus_AH sp018343515	76.7065	99	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303275.1	s__Cytobacillus sp017303275	75.9071	53	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	75.8893	66	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_001591605.1	s__Pseudobacillus badius	75.6178	57	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	98.55	97.77	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:40,324] [INFO] GTDB search result was written to GCF_016909185.1_ASM1690918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:40,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:40,327] [INFO] DFAST_QC result json was written to GCF_016909185.1_ASM1690918v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:40,327] [INFO] DFAST_QC completed!
[2024-01-24 12:07:40,328] [INFO] Total running time: 0h1m41s