[2024-01-24 13:40:46,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference
[2024-01-24 13:40:47,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,397] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f2891b8-7f77-494b-996f-7e030a1815c4/GCF_005930355.1_ASM593035v1_genomic.fna.gz | prodigal -d GCF_005930355.1_ASM593035v1_genomic.fna/cds.fna -a GCF_005930355.1_ASM593035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:04,894] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:04,895] [INFO] Task started: HMMsearch
[2024-01-24 13:41:04,895] [INFO] Running command: hmmsearch --tblout GCF_005930355.1_ASM593035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference/reference_markers.hmm GCF_005930355.1_ASM593035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:05,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:05,230] [INFO] Found 6/6 markers.
[2024-01-24 13:41:05,288] [INFO] Query marker FASTA was written to GCF_005930355.1_ASM593035v1_genomic.fna/markers.fasta
[2024-01-24 13:41:05,288] [INFO] Task started: Blastn
[2024-01-24 13:41:05,288] [INFO] Running command: blastn -query GCF_005930355.1_ASM593035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference/reference_markers.fasta -out GCF_005930355.1_ASM593035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:05,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:05,897] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:05,897] [INFO] Target genome list was writen to GCF_005930355.1_ASM593035v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:05,966] [INFO] Task started: fastANI
[2024-01-24 13:41:05,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f2891b8-7f77-494b-996f-7e030a1815c4/GCF_005930355.1_ASM593035v1_genomic.fna.gz --refList GCF_005930355.1_ASM593035v1_genomic.fna/target_genomes.txt --output GCF_005930355.1_ASM593035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:27,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:27,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:27,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:27,267] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:27,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:27,267] [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 sinopodophylli	strain=CCTCC AB 2016047	GCA_005930355.1	1837342	1837342	type	True	100.0	2313	2316	95	conclusive
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	83.0282	1276	2316	95	below_threshold
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	82.3207	1114	2316	95	below_threshold
Paenibacillus paridis	strain=py1325	GCA_006345825.1	2583376	2583376	type	True	81.5994	1001	2316	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	79.8591	561	2316	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	79.6604	509	2316	95	below_threshold
Paenibacillus castaneae	strain=DSM 19417	GCA_002884445.1	474957	474957	type	True	79.6443	558	2316	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.9038	288	2316	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	77.094	159	2316	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	77.0636	156	2316	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.0532	182	2316	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.8297	106	2316	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.8043	169	2316	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	76.7516	58	2316	95	below_threshold
Paenibacillus curdlanolyticus	strain=YK9	GCA_000179615.1	59840	59840	type	True	76.7161	150	2316	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	76.5944	90	2316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:27,269] [INFO] DFAST Taxonomy check result was written to GCF_005930355.1_ASM593035v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:27,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:27,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:27,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference/checkm_data
[2024-01-24 13:41:27,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:27,339] [INFO] Task started: CheckM
[2024-01-24 13:41:27,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005930355.1_ASM593035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005930355.1_ASM593035v1_genomic.fna/checkm_input GCF_005930355.1_ASM593035v1_genomic.fna/checkm_result
[2024-01-24 13:42:20,319] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:20,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:20,344] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:20,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:20,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005930355.1_ASM593035v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:20,345] [INFO] Task started: Blastn
[2024-01-24 13:42:20,345] [INFO] Running command: blastn -query GCF_005930355.1_ASM593035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3773db6a-cf3b-4684-9353-8a142728cf86/dqc_reference/reference_markers_gtdb.fasta -out GCF_005930355.1_ASM593035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:21,142] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:21,145] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:21,145] [INFO] Target genome list was writen to GCF_005930355.1_ASM593035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:21,180] [INFO] Task started: fastANI
[2024-01-24 13:42:21,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f2891b8-7f77-494b-996f-7e030a1815c4/GCF_005930355.1_ASM593035v1_genomic.fna.gz --refList GCF_005930355.1_ASM593035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005930355.1_ASM593035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:41,809] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:41,834] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:41,834] [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_005930355.1	s__Paenibacillus_C sinopodophylli	100.0	2313	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014192395.1	s__Paenibacillus_C endophyticus	83.0415	1274	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542765.1	s__Paenibacillus_C luteus	82.3264	1115	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006345825.1	s__Paenibacillus_C paridis	81.6204	998	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682865.1	s__Paenibacillus_C sp001682865	81.0	849	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.12	99.12	0.94	0.94	2	-
GCF_012935325.2	s__Paenibacillus_C sp012935325	80.8562	850	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428245.1	s__Paenibacillus_C sp001428245	80.8288	707	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280845.1	s__Paenibacillus_C sp001280845	80.7904	762	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956295.1	s__Paenibacillus_C sp001956295	80.7467	813	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956095.1	s__Paenibacillus_C sp001956095	80.5139	796	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001277345.1	s__Paenibacillus solani	76.7582	59	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.74	96.74	0.91	0.91	2	-
GCF_009789195.1	s__Paenibacillus_T sp009789195	76.7527	152	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179615.1	s__Paenibacillus_T curdlanolyticus	76.7149	150	2316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	75.888	71	2316	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,837] [INFO] GTDB search result was written to GCF_005930355.1_ASM593035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:41,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:41,844] [INFO] DFAST_QC result json was written to GCF_005930355.1_ASM593035v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:41,844] [INFO] DFAST_QC completed!
[2024-01-24 13:42:41,844] [INFO] Total running time: 0h1m56s