[2024-01-25 20:02:35,568] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:35,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:35,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference
[2024-01-25 20:02:36,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:36,841] [INFO] Task started: Prodigal
[2024-01-25 20:02:36,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg80fed2d8-b04d-4799-8ec0-f83c1d339a23/GCF_016612995.1_ASM1661299v1_genomic.fna.gz | prodigal -d GCF_016612995.1_ASM1661299v1_genomic.fna/cds.fna -a GCF_016612995.1_ASM1661299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:44,567] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:44,567] [INFO] Task started: HMMsearch
[2024-01-25 20:02:44,567] [INFO] Running command: hmmsearch --tblout GCF_016612995.1_ASM1661299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference/reference_markers.hmm GCF_016612995.1_ASM1661299v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:44,824] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:44,825] [INFO] Found 6/6 markers.
[2024-01-25 20:02:44,860] [INFO] Query marker FASTA was written to GCF_016612995.1_ASM1661299v1_genomic.fna/markers.fasta
[2024-01-25 20:02:44,860] [INFO] Task started: Blastn
[2024-01-25 20:02:44,860] [INFO] Running command: blastn -query GCF_016612995.1_ASM1661299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference/reference_markers.fasta -out GCF_016612995.1_ASM1661299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:45,446] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:45,449] [INFO] Selected 19 target genomes.
[2024-01-25 20:02:45,450] [INFO] Target genome list was writen to GCF_016612995.1_ASM1661299v1_genomic.fna/target_genomes.txt
[2024-01-25 20:02:45,462] [INFO] Task started: fastANI
[2024-01-25 20:02:45,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg80fed2d8-b04d-4799-8ec0-f83c1d339a23/GCF_016612995.1_ASM1661299v1_genomic.fna.gz --refList GCF_016612995.1_ASM1661299v1_genomic.fna/target_genomes.txt --output GCF_016612995.1_ASM1661299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:57,678] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:57,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:57,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:57,690] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:02:57,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:57,690] [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
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	100.0	1465	1468	95	conclusive
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	84.2419	984	1468	95	below_threshold
Rummeliibacillus pycnus	strain=DSM 15030	GCA_002884495.1	101070	101070	type	True	78.4385	319	1468	95	below_threshold
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	78.1593	275	1468	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	77.9388	162	1468	95	below_threshold
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	77.9223	194	1468	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.9024	223	1468	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	77.9002	194	1468	95	below_threshold
Lysinibacillus composti	strain=DSM 24785	GCA_016908465.1	720633	720633	type	True	77.7999	161	1468	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.7873	165	1468	95	below_threshold
Kurthia zopfii	strain=NCTC10597	GCA_900452285.1	1650	1650	type	True	77.7784	197	1468	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	77.7591	201	1468	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.6746	159	1468	95	below_threshold
Kurthia senegalensis	strain=type strain: JC8E	GCA_000285595.1	1033740	1033740	type	True	77.6306	179	1468	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	77.6267	155	1468	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	77.2107	146	1468	95	below_threshold
Ureibacillus thermosphaericus	strain=DSM 10633	GCA_012396605.1	51173	51173	type	True	77.0264	97	1468	95	below_threshold
Ureibacillus thermosphaericus	strain=DSM 10633	GCA_014202525.1	51173	51173	type	True	76.9748	99	1468	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.4478	66	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:57,692] [INFO] DFAST Taxonomy check result was written to GCF_016612995.1_ASM1661299v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:57,692] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:57,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:57,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference/checkm_data
[2024-01-25 20:02:57,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:57,738] [INFO] Task started: CheckM
[2024-01-25 20:02:57,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016612995.1_ASM1661299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016612995.1_ASM1661299v1_genomic.fna/checkm_input GCF_016612995.1_ASM1661299v1_genomic.fna/checkm_result
[2024-01-25 20:03:25,184] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:25,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:25,203] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:25,203] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:25,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016612995.1_ASM1661299v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:25,204] [INFO] Task started: Blastn
[2024-01-25 20:03:25,204] [INFO] Running command: blastn -query GCF_016612995.1_ASM1661299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82bcc5ae-b780-4a67-906c-afb48b4fc5a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016612995.1_ASM1661299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:25,992] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:25,995] [INFO] Selected 12 target genomes.
[2024-01-25 20:03:25,995] [INFO] Target genome list was writen to GCF_016612995.1_ASM1661299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:26,008] [INFO] Task started: fastANI
[2024-01-25 20:03:26,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg80fed2d8-b04d-4799-8ec0-f83c1d339a23/GCF_016612995.1_ASM1661299v1_genomic.fna.gz --refList GCF_016612995.1_ASM1661299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016612995.1_ASM1661299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:35,984] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:35,992] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:35,992] [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_002813185.1	s__Viridibacillus sp002813185	97.9738	1247	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	conclusive
GCF_001274945.1	s__Viridibacillus arvi	84.2569	982	1468	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_001955655.1	s__Viridibacillus arenosi	84.1671	974	1468	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_003576525.1	s__Rummeliibacillus sp003576525	78.4398	278	1468	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	78.4385	319	1468	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_007896435.1	s__Rummeliibacillus suwonensis	78.1593	275	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
GCF_003143955.1	s__Kurthia zopfii	77.9002	194	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	-
GCF_003991225.1	s__Kurthia intestinigallinarum	77.8622	190	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
GCF_016908465.1	s__Ureibacillus composti	77.7999	161	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003711845.1	s__Ureibacillus halotolerans	77.592	162	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143975.1	s__Kurthia sibirica	77.5321	180	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012396605.1	s__Ureibacillus thermosphaericus	77.0264	97	1468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	99.22	98.33	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:03:35,994] [INFO] GTDB search result was written to GCF_016612995.1_ASM1661299v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:35,994] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:35,997] [INFO] DFAST_QC result json was written to GCF_016612995.1_ASM1661299v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:35,998] [INFO] DFAST_QC completed!
[2024-01-25 20:03:35,998] [INFO] Total running time: 0h1m0s