[2024-01-24 12:21:56,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:56,236] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:56,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference
[2024-01-24 12:21:57,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:57,542] [INFO] Task started: Prodigal
[2024-01-24 12:21:57,543] [INFO] Running command: gunzip -c /var/lib/cwl/stge83028b3-aa1b-4729-b2c6-d9ecdefb0d4a/GCF_003583765.1_ASM358376v1_genomic.fna.gz | prodigal -d GCF_003583765.1_ASM358376v1_genomic.fna/cds.fna -a GCF_003583765.1_ASM358376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:14,181] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:14,181] [INFO] Task started: HMMsearch
[2024-01-24 12:22:14,182] [INFO] Running command: hmmsearch --tblout GCF_003583765.1_ASM358376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference/reference_markers.hmm GCF_003583765.1_ASM358376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:14,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:14,563] [INFO] Found 6/6 markers.
[2024-01-24 12:22:14,642] [INFO] Query marker FASTA was written to GCF_003583765.1_ASM358376v1_genomic.fna/markers.fasta
[2024-01-24 12:22:14,643] [INFO] Task started: Blastn
[2024-01-24 12:22:14,643] [INFO] Running command: blastn -query GCF_003583765.1_ASM358376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference/reference_markers.fasta -out GCF_003583765.1_ASM358376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:15,271] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:15,275] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:15,275] [INFO] Target genome list was writen to GCF_003583765.1_ASM358376v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:15,286] [INFO] Task started: fastANI
[2024-01-24 12:22:15,287] [INFO] Running command: fastANI --query /var/lib/cwl/stge83028b3-aa1b-4729-b2c6-d9ecdefb0d4a/GCF_003583765.1_ASM358376v1_genomic.fna.gz --refList GCF_003583765.1_ASM358376v1_genomic.fna/target_genomes.txt --output GCF_003583765.1_ASM358376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:37,022] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:37,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:37,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:37,038] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:37,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:37,039] [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 nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	100.0	2013	2017	95	conclusive
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	79.7049	587	2017	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	79.4782	498	2017	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	78.5571	429	2017	95	below_threshold
Paenibacillus oryzae	strain=1DrF-4	GCA_001675045.1	1844972	1844972	type	True	78.0438	336	2017	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	77.9973	331	2017	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.9629	367	2017	95	below_threshold
Paenibacillus protaetiae	strain=FW100M-2	GCA_004135365.1	2509456	2509456	type	True	77.6624	269	2017	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	77.6141	315	2017	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.3182	305	2017	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.3122	291	2017	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.2616	222	2017	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.2293	296	2017	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.1664	150	2017	95	below_threshold
Paenibacillus algorifonticola	strain=XJ259	GCA_000971975.1	684063	684063	type	True	77.0858	256	2017	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	77.0751	216	2017	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	77.0553	258	2017	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.979	218	2017	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.6581	158	2017	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.5813	102	2017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:37,041] [INFO] DFAST Taxonomy check result was written to GCF_003583765.1_ASM358376v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:37,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:37,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:37,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference/checkm_data
[2024-01-24 12:22:37,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:37,102] [INFO] Task started: CheckM
[2024-01-24 12:22:37,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583765.1_ASM358376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583765.1_ASM358376v1_genomic.fna/checkm_input GCF_003583765.1_ASM358376v1_genomic.fna/checkm_result
[2024-01-24 12:23:23,557] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:23,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,578] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:23,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:23,579] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583765.1_ASM358376v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:23,579] [INFO] Task started: Blastn
[2024-01-24 12:23:23,579] [INFO] Running command: blastn -query GCF_003583765.1_ASM358376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9df3e4bb-9297-4c7f-9772-3bc2bd297a4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583765.1_ASM358376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,363] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,366] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:24,366] [INFO] Target genome list was writen to GCF_003583765.1_ASM358376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:24,376] [INFO] Task started: fastANI
[2024-01-24 12:23:24,376] [INFO] Running command: fastANI --query /var/lib/cwl/stge83028b3-aa1b-4729-b2c6-d9ecdefb0d4a/GCF_003583765.1_ASM358376v1_genomic.fna.gz --refList GCF_003583765.1_ASM358376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003583765.1_ASM358376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:39,269] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:39,281] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:39,281] [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_003583765.1	s__Paenibacillus_C nanensis	100.0	2013	2017	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_003591485.1	s__Paenibacillus_C sp003591485	79.7409	565	2017	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_003605435.1	s__Paenibacillus_C pinisoli	79.6999	587	2017	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_003388735.1	s__Paenibacillus_C paeoniae	79.4845	496	2017	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_014705655.1	s__Paenibacillus_C sp014705655	79.0677	504	2017	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_000422465.1	s__Paenibacillus_C harenae	78.5474	430	2017	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_003112455.1	s__Paenibacillus_C agaridevorans	78.5201	479	2017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	78.1131	335	2017	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_004000805.1	s__Paenibacillus_C glycanilyticus	78.0019	330	2017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	97.79	97.79	0.90	0.90	2	-
GCF_005222705.1	s__Paenibacillus_C sp005222705	77.7408	327	2017	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_003386535.1	s__Paenibacillus_Z taihuensis	77.2742	221	2017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741035.1	s__Paenibacillus_C sp002741035	77.2332	263	2017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	95.68	95.68	0.84	0.84	2	-
GCF_004000905.1	s__Paenibacillus_O humicus	77.0636	216	2017	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	98.90	98.81	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:39,283] [INFO] GTDB search result was written to GCF_003583765.1_ASM358376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:39,283] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:39,288] [INFO] DFAST_QC result json was written to GCF_003583765.1_ASM358376v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:39,288] [INFO] DFAST_QC completed!
[2024-01-24 12:23:39,288] [INFO] Total running time: 0h1m43s