[2024-01-24 15:18:51,063] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,065] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,065] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference
[2024-01-24 15:18:52,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:52,437] [INFO] Task started: Prodigal
[2024-01-24 15:18:52,437] [INFO] Running command: gunzip -c /var/lib/cwl/stgf96a42c4-b744-481f-8d40-f7976daae309/GCF_007896435.1_ASM789643v1_genomic.fna.gz | prodigal -d GCF_007896435.1_ASM789643v1_genomic.fna/cds.fna -a GCF_007896435.1_ASM789643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:01,002] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:01,002] [INFO] Task started: HMMsearch
[2024-01-24 15:19:01,003] [INFO] Running command: hmmsearch --tblout GCF_007896435.1_ASM789643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference/reference_markers.hmm GCF_007896435.1_ASM789643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:01,323] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:01,325] [INFO] Found 6/6 markers.
[2024-01-24 15:19:01,361] [INFO] Query marker FASTA was written to GCF_007896435.1_ASM789643v1_genomic.fna/markers.fasta
[2024-01-24 15:19:01,362] [INFO] Task started: Blastn
[2024-01-24 15:19:01,362] [INFO] Running command: blastn -query GCF_007896435.1_ASM789643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference/reference_markers.fasta -out GCF_007896435.1_ASM789643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:02,019] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:02,022] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:02,023] [INFO] Target genome list was writen to GCF_007896435.1_ASM789643v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:02,030] [INFO] Task started: fastANI
[2024-01-24 15:19:02,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgf96a42c4-b744-481f-8d40-f7976daae309/GCF_007896435.1_ASM789643v1_genomic.fna.gz --refList GCF_007896435.1_ASM789643v1_genomic.fna/target_genomes.txt --output GCF_007896435.1_ASM789643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:16,207] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:16,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:16,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:16,224] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:16,225] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:16,225] [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
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	100.0	1359	1360	95	conclusive
Rummeliibacillus pycnus	strain=DSM 15030	GCA_002884495.1	101070	101070	type	True	81.1255	620	1360	95	below_threshold
Rummeliibacillus stabekisii	strain=DSM 25578	GCA_014202625.1	241244	241244	type	True	78.9183	275	1360	95	below_threshold
Rummeliibacillus stabekisii	strain=NBRC 104870	GCA_007988965.1	241244	241244	type	True	78.7606	279	1360	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	78.4104	268	1360	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	78.3424	252	1360	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	78.2438	157	1360	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	78.1082	152	1360	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	77.4643	90	1360	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	77.289	93	1360	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	77.1394	124	1360	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.136	125	1360	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.1448	54	1360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:16,227] [INFO] DFAST Taxonomy check result was written to GCF_007896435.1_ASM789643v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:16,227] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:16,227] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:16,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference/checkm_data
[2024-01-24 15:19:16,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:16,268] [INFO] Task started: CheckM
[2024-01-24 15:19:16,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007896435.1_ASM789643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007896435.1_ASM789643v1_genomic.fna/checkm_input GCF_007896435.1_ASM789643v1_genomic.fna/checkm_result
[2024-01-24 15:19:47,362] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:47,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:47,395] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:47,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:47,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007896435.1_ASM789643v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:47,397] [INFO] Task started: Blastn
[2024-01-24 15:19:47,397] [INFO] Running command: blastn -query GCF_007896435.1_ASM789643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbd35a53-88f8-4393-8639-1aaa7b68503f/dqc_reference/reference_markers_gtdb.fasta -out GCF_007896435.1_ASM789643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:48,211] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:48,217] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:48,217] [INFO] Target genome list was writen to GCF_007896435.1_ASM789643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:48,226] [INFO] Task started: fastANI
[2024-01-24 15:19:48,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgf96a42c4-b744-481f-8d40-f7976daae309/GCF_007896435.1_ASM789643v1_genomic.fna.gz --refList GCF_007896435.1_ASM789643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007896435.1_ASM789643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:59,473] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:59,485] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:59,486] [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_007896435.1	s__Rummeliibacillus suwonensis	100.0	1359	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	conclusive
GCF_003576525.1	s__Rummeliibacillus sp003576525	81.7625	656	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.66	98.66	0.89	0.89	2	-
GCF_002884495.1	s__Rummeliibacillus pycnus	81.114	621	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988965.1	s__Rummeliibacillus stabekisii	78.745	280	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.11	96.96	0.93	0.90	5	-
GCF_002813185.1	s__Viridibacillus sp002813185	78.4616	262	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
GCF_001274945.1	s__Viridibacillus arvi	78.3427	252	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	95.96	95.96	0.91	0.91	2	-
GCF_000285595.1	s__Kurthia senegalensis	78.2438	157	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001955655.1	s__Viridibacillus arenosi	78.2079	254	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	99.71	99.53	0.97	0.96	4	-
GCF_001939075.1	s__Paenisporosarcina indica	77.4643	90	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643595.1	s__Metalysinibacillus alkalisoli	77.4223	91	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Metalysinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217295.1	s__Ureibacillus chungkukjangi	77.1621	124	1360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:59,487] [INFO] GTDB search result was written to GCF_007896435.1_ASM789643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:59,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:59,491] [INFO] DFAST_QC result json was written to GCF_007896435.1_ASM789643v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:59,491] [INFO] DFAST_QC completed!
[2024-01-24 15:19:59,491] [INFO] Total running time: 0h1m8s