[2024-01-25 20:06:05,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:05,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:05,586] [INFO] DQC Reference Directory: /var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference
[2024-01-25 20:06:06,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:06,710] [INFO] Task started: Prodigal
[2024-01-25 20:06:06,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg6abaef0a-8e6b-4c80-b1a7-2cc68e77fe8e/GCF_017874255.1_ASM1787425v1_genomic.fna.gz | prodigal -d GCF_017874255.1_ASM1787425v1_genomic.fna/cds.fna -a GCF_017874255.1_ASM1787425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:15,210] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:15,211] [INFO] Task started: HMMsearch
[2024-01-25 20:06:15,211] [INFO] Running command: hmmsearch --tblout GCF_017874255.1_ASM1787425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference/reference_markers.hmm GCF_017874255.1_ASM1787425v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:15,462] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:15,463] [INFO] Found 6/6 markers.
[2024-01-25 20:06:15,495] [INFO] Query marker FASTA was written to GCF_017874255.1_ASM1787425v1_genomic.fna/markers.fasta
[2024-01-25 20:06:15,495] [INFO] Task started: Blastn
[2024-01-25 20:06:15,495] [INFO] Running command: blastn -query GCF_017874255.1_ASM1787425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference/reference_markers.fasta -out GCF_017874255.1_ASM1787425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:16,066] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:16,069] [INFO] Selected 25 target genomes.
[2024-01-25 20:06:16,069] [INFO] Target genome list was writen to GCF_017874255.1_ASM1787425v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:16,107] [INFO] Task started: fastANI
[2024-01-25 20:06:16,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg6abaef0a-8e6b-4c80-b1a7-2cc68e77fe8e/GCF_017874255.1_ASM1787425v1_genomic.fna.gz --refList GCF_017874255.1_ASM1787425v1_genomic.fna/target_genomes.txt --output GCF_017874255.1_ASM1787425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:41,118] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:41,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:41,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:41,130] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:06:41,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:06:41,131] [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 shirakamiensis	strain=DSM 26806	GCA_017874255.1	1265935	1265935	type	True	100.0	1356	1356	95	conclusive
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	78.4513	242	1356	95	below_threshold
Paenibacillus tuaregi	strain=Marseille-P2472	GCA_900086655.1	1816681	1816681	type	True	78.3297	232	1356	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	77.7974	106	1356	95	below_threshold
Paenibacillus massiliensis subsp. panacisoli	strain=DSM 21345	GCA_000426545.1	363858	225917	type	True	77.7137	74	1356	95	below_threshold
Paenibacillus sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	77.5577	82	1356	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	77.542	139	1356	95	below_threshold
Paenibacillus physcomitrellae	strain=XB	GCA_002240225.1	1619311	1619311	type	True	77.5009	105	1356	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	77.4969	97	1356	95	below_threshold
Paenibacillus tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	77.4469	64	1356	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.4445	95	1356	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	77.3799	93	1356	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.3627	93	1356	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	77.2682	51	1356	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.1645	53	1356	95	below_threshold
Paenibacillus massiliensis	strain=DSM 16942	GCA_000377505.1	225917	225917	type	True	77.1578	81	1356	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	77.1527	62	1356	95	below_threshold
Paenibacillus arenosi	strain=CAU 1523	GCA_014841135.1	2774142	2774142	type	True	77.1041	51	1356	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	77.0405	75	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:41,132] [INFO] DFAST Taxonomy check result was written to GCF_017874255.1_ASM1787425v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:41,133] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:41,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:41,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference/checkm_data
[2024-01-25 20:06:41,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:41,175] [INFO] Task started: CheckM
[2024-01-25 20:06:41,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874255.1_ASM1787425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874255.1_ASM1787425v1_genomic.fna/checkm_input GCF_017874255.1_ASM1787425v1_genomic.fna/checkm_result
[2024-01-25 20:07:11,091] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:11,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:11,109] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:11,109] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:11,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874255.1_ASM1787425v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:11,109] [INFO] Task started: Blastn
[2024-01-25 20:07:11,110] [INFO] Running command: blastn -query GCF_017874255.1_ASM1787425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga254aaf4-e169-417e-85a1-21459becd21a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874255.1_ASM1787425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:11,843] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:11,849] [INFO] Selected 24 target genomes.
[2024-01-25 20:07:11,849] [INFO] Target genome list was writen to GCF_017874255.1_ASM1787425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:11,879] [INFO] Task started: fastANI
[2024-01-25 20:07:11,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg6abaef0a-8e6b-4c80-b1a7-2cc68e77fe8e/GCF_017874255.1_ASM1787425v1_genomic.fna.gz --refList GCF_017874255.1_ASM1787425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874255.1_ASM1787425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:37,051] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:37,065] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:37,065] [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_017874255.1	s__Paenibacillus_A shirakamiensis	100.0	1356	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003994465.1	s__Paenibacillus_A zeisoli	78.4746	242	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900086655.1	s__Paenibacillus_A tuaregi	78.3292	233	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.53	97.06	0.96	0.92	3	-
GCF_018614975.1	s__Paenibacillus polymyxa_E	77.9328	107	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	77.8103	105	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426545.1	s__Paenibacillus panacisoli	77.727	72	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.1083	98.22	98.22	0.93	0.93	2	-
GCF_002968835.1	s__Paenibacillus sp002968835	77.6705	95	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268635.1	s__Paenibacillus sp003268635	77.6552	99	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955535.1	s__Paenibacillus sp001955535	77.6426	84	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.62	98.62	0.85	0.85	2	-
GCF_001570725.1	s__Paenibacillus amylolyticus_A	77.6289	108	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.59	97.52	0.92	0.91	3	-
GCF_002240225.1	s__Paenibacillus_A physcomitrellae	77.5417	105	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014639155.1	s__Paenibacillus_A segetis	77.5404	137	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359935.1	s__Paenibacillus xylanilyticus	77.492	97	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614185.1	s__Paenibacillus_A aceti	77.3964	97	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000758725.1	s__Paenibacillus odorifer	77.3799	93	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
GCF_012912005.1	s__Paenibacillus sp012912005	77.3741	101	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007680605.1	s__Paenibacillus xylanexedens_B	77.3596	89	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.13	99.13	0.96	0.96	2	-
GCF_016908805.1	s__Paenibacillus_J nicotianae	77.3334	75	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955855.1	s__Paenibacillus sp001955855	77.2995	112	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.7262	N/A	N/A	N/A	N/A	1	-
GCF_000377505.1	s__Paenibacillus massiliensis	77.1916	82	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.1083	98.51	98.51	0.94	0.94	2	-
GCF_003719335.1	s__Paenibacillus amylolyticus_D	77.1077	93	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721045.1	s__Paenibacillus_J nuruki	77.0405	75	1356	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:37,069] [INFO] GTDB search result was written to GCF_017874255.1_ASM1787425v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:37,069] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:37,073] [INFO] DFAST_QC result json was written to GCF_017874255.1_ASM1787425v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:37,073] [INFO] DFAST_QC completed!
[2024-01-25 20:07:37,073] [INFO] Total running time: 0h1m31s