[2024-01-24 13:32:41,983] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference
[2024-01-24 13:32:43,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,269] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f974e4e-9044-451f-908f-4a6f72ae90a8/GCF_019443105.1_ASM1944310v1_genomic.fna.gz | prodigal -d GCF_019443105.1_ASM1944310v1_genomic.fna/cds.fna -a GCF_019443105.1_ASM1944310v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:59,859] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:59,859] [INFO] Task started: HMMsearch
[2024-01-24 13:32:59,860] [INFO] Running command: hmmsearch --tblout GCF_019443105.1_ASM1944310v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference/reference_markers.hmm GCF_019443105.1_ASM1944310v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:00,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:00,221] [INFO] Found 6/6 markers.
[2024-01-24 13:33:00,274] [INFO] Query marker FASTA was written to GCF_019443105.1_ASM1944310v1_genomic.fna/markers.fasta
[2024-01-24 13:33:00,274] [INFO] Task started: Blastn
[2024-01-24 13:33:00,274] [INFO] Running command: blastn -query GCF_019443105.1_ASM1944310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference/reference_markers.fasta -out GCF_019443105.1_ASM1944310v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:00,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:00,924] [INFO] Selected 24 target genomes.
[2024-01-24 13:33:00,924] [INFO] Target genome list was writen to GCF_019443105.1_ASM1944310v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:00,974] [INFO] Task started: fastANI
[2024-01-24 13:33:00,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f974e4e-9044-451f-908f-4a6f72ae90a8/GCF_019443105.1_ASM1944310v1_genomic.fna.gz --refList GCF_019443105.1_ASM1944310v1_genomic.fna/target_genomes.txt --output GCF_019443105.1_ASM1944310v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:30,036] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:30,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:30,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:30,107] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:30,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:30,107] [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 oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	100.0	1857	1858	95	conclusive
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	78.0402	262	1858	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	78.0246	299	1858	95	below_threshold
Paenibacillus nasutitermitis	strain=CGMCC 1.15178	GCA_014641075.1	1652958	1652958	type	True	77.995	296	1858	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	77.9868	264	1858	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.9802	308	1858	95	below_threshold
Paenibacillus baekrokdamisoli	strain=KCTC 33723	GCA_003945345.1	1712516	1712516	type	True	77.9757	278	1858	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.9353	298	1858	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.8797	294	1858	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	77.8631	273	1858	95	below_threshold
Paenibacillus baekrokdamisoli	strain=CECT 8890	GCA_014191785.1	1712516	1712516	type	True	77.8611	270	1858	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.8595	267	1858	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.6914	294	1858	95	below_threshold
Paenibacillus algorifonticola	strain=CGMCC 1.10223	GCA_900112925.1	684063	684063	type	True	77.5338	195	1858	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	77.3112	171	1858	95	below_threshold
Paenibacillus sambharensis	strain=SMB1	GCA_003233845.1	1803190	1803190	type	True	77.284	189	1858	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.0687	86	1858	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.0479	83	1858	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	77.0406	169	1858	95	below_threshold
Paenibacillus tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	76.7629	106	1858	95	below_threshold
Paenibacillus donghaensis	strain=KCTC 13049	GCA_002192415.1	414771	414771	type	True	76.5456	105	1858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:30,117] [INFO] DFAST Taxonomy check result was written to GCF_019443105.1_ASM1944310v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:30,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:30,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:30,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference/checkm_data
[2024-01-24 13:33:30,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:30,264] [INFO] Task started: CheckM
[2024-01-24 13:33:30,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019443105.1_ASM1944310v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019443105.1_ASM1944310v1_genomic.fna/checkm_input GCF_019443105.1_ASM1944310v1_genomic.fna/checkm_result
[2024-01-24 13:34:21,656] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:21,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:21,679] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:21,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:21,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019443105.1_ASM1944310v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:21,680] [INFO] Task started: Blastn
[2024-01-24 13:34:21,680] [INFO] Running command: blastn -query GCF_019443105.1_ASM1944310v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b55a4c1-6e84-47dc-9ac2-2486d5d03366/dqc_reference/reference_markers_gtdb.fasta -out GCF_019443105.1_ASM1944310v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:22,507] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:22,512] [INFO] Selected 27 target genomes.
[2024-01-24 13:34:22,513] [INFO] Target genome list was writen to GCF_019443105.1_ASM1944310v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:22,536] [INFO] Task started: fastANI
[2024-01-24 13:34:22,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f974e4e-9044-451f-908f-4a6f72ae90a8/GCF_019443105.1_ASM1944310v1_genomic.fna.gz --refList GCF_019443105.1_ASM1944310v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019443105.1_ASM1944310v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:51,728] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:51,753] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:34:51,754] [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_009909195.1	s__Paenibacillus_Z sacheonensis	78.0539	261	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	78.0486	297	1858	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_900110075.1	s__Paenibacillus_Z sp900110075	78.0132	249	1858	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_014641075.1	s__Paenibacillus_Z nasutitermitis	78.0066	295	1858	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_016908135.1	s__Paenibacillus_Z mendelii	78.0023	308	1858	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_003945345.1	s__Paenibacillus_Z baekrokdamisoli	77.9801	277	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004342525.1	s__Paenibacillus_Z sp004342525	77.9357	258	1858	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_010119935.1	s__Paenibacillus_Z lycopersici	77.9341	296	1858	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_003386535.1	s__Paenibacillus_Z taihuensis	77.9322	278	1858	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_900116125.1	s__Paenibacillus_Z sp900116125	77.8982	278	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_003268025.1	s__Paenibacillus_Z montanisoli	77.8839	293	1858	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_008124765.1	s__Paenibacillus_Z methanolicus	77.8751	272	1858	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_009737085.1	s__Paenibacillus_C sp009737085	77.7118	179	1858	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_009909185.1	s__Paenibacillus_Z glycinis	77.6942	293	1858	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_001682865.1	s__Paenibacillus_C sp001682865	77.437	205	1858	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_001956295.1	s__Paenibacillus_C sp001956295	77.4224	149	1858	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_012935325.2	s__Paenibacillus_C sp012935325	77.3638	208	1858	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_003583765.1	s__Paenibacillus_C nanensis	77.3145	170	1858	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_003233845.1	s__Paenibacillus_I sambharensis	77.2971	190	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345425.1	s__Paenibacillus_C sp004345425	77.1637	192	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_001280845.1	s__Paenibacillus_C sp001280845	77.1373	166	1858	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	77.1134	185	1858	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_011761355.1	s__Paenibacillus_C lupini	77.067	166	1858	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	77.0236	197	1858	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_014705605.1	s__Paenibacillus_D sp014705605	76.6078	138	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918005.1	s__MSJ-34 sp018918005	76.4006	101	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266915.1	s__Paenibacillus_B sp900539405	76.212	113	1858	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	99.54	99.32	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:51,755] [INFO] GTDB search result was written to GCF_019443105.1_ASM1944310v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:51,756] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:51,761] [INFO] DFAST_QC result json was written to GCF_019443105.1_ASM1944310v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:51,761] [INFO] DFAST_QC completed!
[2024-01-24 13:34:51,761] [INFO] Total running time: 0h2m10s