[2024-01-25 18:12:50,840] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:50,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:50,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference
[2024-01-25 18:12:52,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:52,012] [INFO] Task started: Prodigal
[2024-01-25 18:12:52,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5e75bd8-4df8-49f6-bedd-a9452eedb43a/GCF_000426545.1_ASM42654v1_genomic.fna.gz | prodigal -d GCF_000426545.1_ASM42654v1_genomic.fna/cds.fna -a GCF_000426545.1_ASM42654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:06,552] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:06,552] [INFO] Task started: HMMsearch
[2024-01-25 18:13:06,552] [INFO] Running command: hmmsearch --tblout GCF_000426545.1_ASM42654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference/reference_markers.hmm GCF_000426545.1_ASM42654v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:06,894] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:06,895] [INFO] Found 6/6 markers.
[2024-01-25 18:13:06,952] [INFO] Query marker FASTA was written to GCF_000426545.1_ASM42654v1_genomic.fna/markers.fasta
[2024-01-25 18:13:06,953] [INFO] Task started: Blastn
[2024-01-25 18:13:06,953] [INFO] Running command: blastn -query GCF_000426545.1_ASM42654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference/reference_markers.fasta -out GCF_000426545.1_ASM42654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:07,511] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:07,514] [INFO] Selected 25 target genomes.
[2024-01-25 18:13:07,514] [INFO] Target genome list was writen to GCF_000426545.1_ASM42654v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:07,527] [INFO] Task started: fastANI
[2024-01-25 18:13:07,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e75bd8-4df8-49f6-bedd-a9452eedb43a/GCF_000426545.1_ASM42654v1_genomic.fna.gz --refList GCF_000426545.1_ASM42654v1_genomic.fna/target_genomes.txt --output GCF_000426545.1_ASM42654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:33,061] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:33,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:33,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:33,075] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:13:33,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:33,075] [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 massiliensis subsp. panacisoli	strain=DSM 21345	GCA_000426545.1	363858	225917	type	True	100.0	2083	2085	95	conclusive
Paenibacillus massiliensis	strain=DSM 16942	GCA_000377505.1	225917	225917	type	True	96.1083	1808	2085	95	conclusive
Paenibacillus kribbensis	strain=AM49	GCA_002240415.1	172713	172713	type	True	77.7413	251	2085	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	77.7186	140	2085	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.684	117	2085	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	77.6608	216	2085	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	77.6511	228	2085	95	below_threshold
Paenibacillus peoriae	strain=KCTC 3763	GCA_000236805.2	59893	59893	suspected-type	True	77.6398	255	2085	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_000217775.1	1406	1406	type	True	77.6374	226	2085	95	below_threshold
Paenibacillus polymyxa	strain=NCTC10343	GCA_900454525.1	1406	1406	type	True	77.633	231	2085	95	below_threshold
Paenibacillus maysiensis	strain=1-49	GCA_000520815.1	1155954	1155954	type	True	77.5152	237	2085	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	77.4202	131	2085	95	below_threshold
Paenibacillus barcinonensis	strain=CECT 7022	GCA_003217495.1	198119	198119	type	True	77.4067	192	2085	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	77.3327	209	2085	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.3082	148	2085	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	77.2911	178	2085	95	below_threshold
Paenibacillus amylolyticus	strain=NBRC 15957	GCA_004001025.1	1451	1451	suspected-type	True	77.2802	204	2085	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.2702	111	2085	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	77.0936	149	2085	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	76.9599	156	2085	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	76.9494	129	2085	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.6133	69	2085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:33,077] [INFO] DFAST Taxonomy check result was written to GCF_000426545.1_ASM42654v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:33,077] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:33,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:33,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference/checkm_data
[2024-01-25 18:13:33,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:33,141] [INFO] Task started: CheckM
[2024-01-25 18:13:33,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000426545.1_ASM42654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000426545.1_ASM42654v1_genomic.fna/checkm_input GCF_000426545.1_ASM42654v1_genomic.fna/checkm_result
[2024-01-25 18:14:17,826] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:17,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:17,845] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:17,845] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:17,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000426545.1_ASM42654v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:17,846] [INFO] Task started: Blastn
[2024-01-25 18:14:17,846] [INFO] Running command: blastn -query GCF_000426545.1_ASM42654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3572aec1-7409-4821-9fca-77bf497eb1a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000426545.1_ASM42654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:18,630] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:18,633] [INFO] Selected 24 target genomes.
[2024-01-25 18:14:18,633] [INFO] Target genome list was writen to GCF_000426545.1_ASM42654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:18,655] [INFO] Task started: fastANI
[2024-01-25 18:14:18,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5e75bd8-4df8-49f6-bedd-a9452eedb43a/GCF_000426545.1_ASM42654v1_genomic.fna.gz --refList GCF_000426545.1_ASM42654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000426545.1_ASM42654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:44,702] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:44,716] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:44,716] [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_000426545.1	s__Paenibacillus panacisoli	100.0	2083	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.1083	98.22	98.22	0.93	0.93	2	conclusive
GCF_000377505.1	s__Paenibacillus massiliensis	96.1016	1808	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.1083	98.51	98.51	0.94	0.94	2	-
GCF_006874425.1	s__Paenibacillus ottowii	77.8568	247	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.10	96.87	0.92	0.88	5	-
GCF_000235585.1	s__Paenibacillus terrae_B	77.8549	255	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240415.1	s__Paenibacillus kribbensis	77.7706	252	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.18	95.13	0.90	0.86	4	-
GCF_000943545.1	s__Paenibacillus terrae_A	77.6701	243	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001709075.1	s__Paenibacillus polymyxa_D	77.6445	229	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.80	97.93	0.93	0.90	8	-
GCF_000236805.1	s__Paenibacillus peoriae	77.6425	254	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719045.1	s__Paenibacillus polymyxa_B	77.5904	235	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.14	95.58	0.87	0.84	27	-
GCF_015710975.1	s__Paenibacillus polymyxa	77.5755	227	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.54	98.07	0.94	0.89	44	-
GCF_005217525.1	s__Paenibacillus terrae_C	77.5726	230	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287275.1	s__Paenibacillus taichungensis_A	77.5455	190	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002573715.1	s__Paenibacillus sp002573715	77.5325	162	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.81	0.89	0.84	4	-
GCF_000520815.1	s__Paenibacillus maysiensis	77.5159	236	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.32	95.30	0.82	0.80	4	-
GCF_000316035.1	s__Paenibacillus sp000316035	77.4175	188	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.8348	N/A	N/A	N/A	N/A	1	-
GCF_002741055.1	s__Paenibacillus ihbetae	77.4124	130	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.87	98.87	0.95	0.95	2	-
GCF_003217495.1	s__Paenibacillus barcinonensis	77.4081	192	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001955855.1	s__Paenibacillus sp001955855	77.3337	187	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.7262	N/A	N/A	N/A	N/A	1	-
GCF_001908275.1	s__Paenibacillus xylanexedens_A	77.316	209	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.2155	N/A	N/A	N/A	N/A	1	-
GCF_900102085.1	s__Paenibacillus polysaccharolyticus	77.2883	179	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.73	97.72	0.92	0.92	4	-
GCF_013204885.1	s__Paenibacillus tritici	76.9571	155	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
GCF_003994465.1	s__Paenibacillus_A zeisoli	76.9494	129	2085	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_002272015.1	s__Paenibacillus campinasensis	76.8449	145	2085	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:44,717] [INFO] GTDB search result was written to GCF_000426545.1_ASM42654v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:44,719] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:44,725] [INFO] DFAST_QC result json was written to GCF_000426545.1_ASM42654v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:44,725] [INFO] DFAST_QC completed!
[2024-01-25 18:14:44,725] [INFO] Total running time: 0h1m54s