[2024-01-24 15:02:07,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference
[2024-01-24 15:02:09,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,602] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d996139-f19b-4ea9-9630-c6ef8f02aa95/GCF_016424485.1_ASM1642448v1_genomic.fna.gz | prodigal -d GCF_016424485.1_ASM1642448v1_genomic.fna/cds.fna -a GCF_016424485.1_ASM1642448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:23,357] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:23,358] [INFO] Task started: HMMsearch
[2024-01-24 15:02:23,358] [INFO] Running command: hmmsearch --tblout GCF_016424485.1_ASM1642448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference/reference_markers.hmm GCF_016424485.1_ASM1642448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:23,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:23,623] [INFO] Found 6/6 markers.
[2024-01-24 15:02:23,672] [INFO] Query marker FASTA was written to GCF_016424485.1_ASM1642448v1_genomic.fna/markers.fasta
[2024-01-24 15:02:23,672] [INFO] Task started: Blastn
[2024-01-24 15:02:23,673] [INFO] Running command: blastn -query GCF_016424485.1_ASM1642448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference/reference_markers.fasta -out GCF_016424485.1_ASM1642448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:24,311] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:24,316] [INFO] Selected 27 target genomes.
[2024-01-24 15:02:24,316] [INFO] Target genome list was writen to GCF_016424485.1_ASM1642448v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:24,328] [INFO] Task started: fastANI
[2024-01-24 15:02:24,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d996139-f19b-4ea9-9630-c6ef8f02aa95/GCF_016424485.1_ASM1642448v1_genomic.fna.gz --refList GCF_016424485.1_ASM1642448v1_genomic.fna/target_genomes.txt --output GCF_016424485.1_ASM1642448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:51,156] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:51,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:51,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:51,174] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:51,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:51,175] [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 roseus	strain=MAHUQ-46	GCA_016424485.1	2798579	2798579	type	True	100.0	1734	1737	95	conclusive
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	82.9241	1099	1737	95	below_threshold
Paenibacillus abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	77.8481	200	1737	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	77.7577	156	1737	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	77.2129	128	1737	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.1649	157	1737	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	77.1215	75	1737	95	below_threshold
Paenibacillus oryzae	strain=1DrF-4	GCA_001675045.1	1844972	1844972	type	True	77.0085	136	1737	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.9934	123	1737	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	76.8896	140	1737	95	below_threshold
Paenibacillus harenae	strain=DSM 16969	GCA_000422465.1	306543	306543	type	True	76.8735	143	1737	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.8563	112	1737	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.8041	132	1737	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.7795	114	1737	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	76.6734	117	1737	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	76.6538	118	1737	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.6304	104	1737	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.5504	104	1737	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	76.5371	122	1737	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.3082	74	1737	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	76.1752	77	1737	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	76.1178	110	1737	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	75.9339	96	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:51,177] [INFO] DFAST Taxonomy check result was written to GCF_016424485.1_ASM1642448v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:51,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:51,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:51,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference/checkm_data
[2024-01-24 15:02:51,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:51,228] [INFO] Task started: CheckM
[2024-01-24 15:02:51,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016424485.1_ASM1642448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016424485.1_ASM1642448v1_genomic.fna/checkm_input GCF_016424485.1_ASM1642448v1_genomic.fna/checkm_result
[2024-01-24 15:03:37,171] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:37,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 15.58%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:37,196] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:37,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:37,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016424485.1_ASM1642448v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:37,197] [INFO] Task started: Blastn
[2024-01-24 15:03:37,197] [INFO] Running command: blastn -query GCF_016424485.1_ASM1642448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f96a770-3813-4343-bebf-6a1fa8c76dd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016424485.1_ASM1642448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:38,043] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:38,046] [INFO] Selected 28 target genomes.
[2024-01-24 15:03:38,047] [INFO] Target genome list was writen to GCF_016424485.1_ASM1642448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:38,069] [INFO] Task started: fastANI
[2024-01-24 15:03:38,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d996139-f19b-4ea9-9630-c6ef8f02aa95/GCF_016424485.1_ASM1642448v1_genomic.fna.gz --refList GCF_016424485.1_ASM1642448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016424485.1_ASM1642448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:07,898] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:07,918] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:07,918] [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_016424485.1	s__Paenibacillus_D sp016424485	100.0	1734	1737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422505.1	s__Paenibacillus_D pinihumi	82.9163	1100	1737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	99.89	99.89	1.00	1.00	2	-
GCF_014640295.1	s__Paenibacillus_D abyssi	77.8481	200	1737	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_005222705.1	s__Paenibacillus_C sp005222705	77.2724	154	1737	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_014641555.1	s__Paenibacillus_C radicis	77.2433	180	1737	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_000378385.1	s__Paenibacillus_D daejeonensis	77.1621	149	1737	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_000513275.1	s__Paenibacillus_C gorillae	77.1546	156	1737	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	77.1258	147	1737	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_003112455.1	s__Paenibacillus_C agaridevorans	77.0586	120	1737	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_900116125.1	s__Paenibacillus_Z sp900116125	77.0157	114	1737	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_001675045.1	s__Paenibacillus_C oryzae	76.9911	137	1737	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_010119935.1	s__Paenibacillus_Z lycopersici	76.9909	123	1737	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_012935325.2	s__Paenibacillus_C sp012935325	76.8418	136	1737	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_001719045.1	s__Paenibacillus polymyxa_B	76.7928	65	1737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.14	95.58	0.87	0.84	27	-
GCF_004000805.1	s__Paenibacillus_C glycanilyticus	76.7861	133	1737	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_008124765.1	s__Paenibacillus_Z methanolicus	76.7795	114	1737	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_004342525.1	s__Paenibacillus_Z sp004342525	76.747	112	1737	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_009909195.1	s__Paenibacillus_Z sacheonensis	76.6734	117	1737	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_900110075.1	s__Paenibacillus_Z sp900110075	76.6204	108	1737	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_004000825.1	s__Paenibacillus_T kobensis	76.5915	128	1737	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_000598065.1	s__Paenibacillus_I darwinianus	76.5504	104	1737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	99.89	99.87	0.94	0.94	3	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	76.5371	122	1737	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_018998565.1	s__Paenibacillus_G sp018998565	76.488	99	1737	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_001709075.1	s__Paenibacillus polymyxa_D	76.3801	52	1737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.80	97.93	0.93	0.90	8	-
GCF_000758525.1	s__Paenibacillus sp000758525	76.2292	100	1737	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_013266915.1	s__Paenibacillus_B sp900539405	76.0508	82	1737	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 15:04:07,920] [INFO] GTDB search result was written to GCF_016424485.1_ASM1642448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:07,921] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:07,926] [INFO] DFAST_QC result json was written to GCF_016424485.1_ASM1642448v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:07,926] [INFO] DFAST_QC completed!
[2024-01-24 15:04:07,926] [INFO] Total running time: 0h2m0s