[2024-01-24 11:19:49,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:49,017] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:49,017] [INFO] DQC Reference Directory: /var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference
[2024-01-24 11:19:50,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,251] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,251] [INFO] Running command: gunzip -c /var/lib/cwl/stga2beba57-09f0-44fd-9573-f7aa41ee0cad/GCF_004000985.1_ASM400098v1_genomic.fna.gz | prodigal -d GCF_004000985.1_ASM400098v1_genomic.fna/cds.fna -a GCF_004000985.1_ASM400098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:04,992] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:04,993] [INFO] Task started: HMMsearch
[2024-01-24 11:20:04,993] [INFO] Running command: hmmsearch --tblout GCF_004000985.1_ASM400098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference/reference_markers.hmm GCF_004000985.1_ASM400098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:05,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:05,308] [INFO] Found 6/6 markers.
[2024-01-24 11:20:05,363] [INFO] Query marker FASTA was written to GCF_004000985.1_ASM400098v1_genomic.fna/markers.fasta
[2024-01-24 11:20:05,363] [INFO] Task started: Blastn
[2024-01-24 11:20:05,363] [INFO] Running command: blastn -query GCF_004000985.1_ASM400098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference/reference_markers.fasta -out GCF_004000985.1_ASM400098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:05,986] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:05,991] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:05,991] [INFO] Target genome list was writen to GCF_004000985.1_ASM400098v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:06,009] [INFO] Task started: fastANI
[2024-01-24 11:20:06,009] [INFO] Running command: fastANI --query /var/lib/cwl/stga2beba57-09f0-44fd-9573-f7aa41ee0cad/GCF_004000985.1_ASM400098v1_genomic.fna.gz --refList GCF_004000985.1_ASM400098v1_genomic.fna/target_genomes.txt --output GCF_004000985.1_ASM400098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:27,149] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:27,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:27,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:27,169] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:27,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:27,169] [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
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	100.0	1773	1782	95	conclusive
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	78.9041	459	1782	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	78.7833	445	1782	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	78.7267	425	1782	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	78.5772	457	1782	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	78.512	421	1782	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	78.1388	373	1782	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.7636	314	1782	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.6325	286	1782	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.164	140	1782	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	77.0136	170	1782	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	76.7047	227	1782	95	below_threshold
Paenibacillus periandrae	strain=PM10	GCA_022458865.1	1761741	1761741	type	True	76.5411	145	1782	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	76.5188	80	1782	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	76.2529	97	1782	95	below_threshold
Paenibacillus cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	76.2283	101	1782	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.1978	96	1782	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.0172	86	1782	95	below_threshold
Paenibacillus senegalimassiliensis	strain=SIT18	GCA_001486585.1	1737426	1737426	type	True	76.0118	56	1782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:27,171] [INFO] DFAST Taxonomy check result was written to GCF_004000985.1_ASM400098v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:27,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:27,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:27,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference/checkm_data
[2024-01-24 11:20:27,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:27,222] [INFO] Task started: CheckM
[2024-01-24 11:20:27,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004000985.1_ASM400098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004000985.1_ASM400098v1_genomic.fna/checkm_input GCF_004000985.1_ASM400098v1_genomic.fna/checkm_result
[2024-01-24 11:21:12,182] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:12,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:12,206] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:12,207] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:12,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004000985.1_ASM400098v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:12,208] [INFO] Task started: Blastn
[2024-01-24 11:21:12,208] [INFO] Running command: blastn -query GCF_004000985.1_ASM400098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee9512e5-058d-4c79-985a-0cfbc17241ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_004000985.1_ASM400098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:13,042] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:13,046] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:13,046] [INFO] Target genome list was writen to GCF_004000985.1_ASM400098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:13,057] [INFO] Task started: fastANI
[2024-01-24 11:21:13,058] [INFO] Running command: fastANI --query /var/lib/cwl/stga2beba57-09f0-44fd-9573-f7aa41ee0cad/GCF_004000985.1_ASM400098v1_genomic.fna.gz --refList GCF_004000985.1_ASM400098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004000985.1_ASM400098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:28,807] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:28,831] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:28,831] [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_004000985.1	s__Paenibacillus_G validus	100.0	1773	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	conclusive
GCF_004000785.1	s__Paenibacillus_G ehimensis	78.9222	457	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	78.8607	420	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	78.7833	445	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
GCF_004000865.1	s__Paenibacillus_G elgii	78.7267	425	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_018998565.1	s__Paenibacillus_G sp018998565	78.6646	445	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100345.1	s__Paenibacillus_G tianmuensis	78.512	421	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910594985.1	s__Paenibacillus_G sp910594985	78.1428	372	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_910593845.1	s__Paenibacillus_G solanacearum	78.0571	395	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250655.1	s__Paenibacillus_G mucilaginosus	77.7999	364	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.86	98.79	0.96	0.95	3	-
GCF_000829455.1	s__VKM-B-2647 sp000829455	77.3636	243	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411255.1	s__Paenibacillus_F sp000411255	76.8854	156	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_F	95.0	99.59	98.79	0.98	0.94	4	-
GCF_005765165.1	s__Paenibacillus_AE antri	76.7665	154	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345425.1	s__Paenibacillus_C sp004345425	76.46	106	1782	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:28,833] [INFO] GTDB search result was written to GCF_004000985.1_ASM400098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:28,833] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:28,837] [INFO] DFAST_QC result json was written to GCF_004000985.1_ASM400098v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:28,837] [INFO] DFAST_QC completed!
[2024-01-24 11:21:28,837] [INFO] Total running time: 0h1m40s