[2024-01-24 12:46:35,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,233] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,233] [INFO] DQC Reference Directory: /var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference
[2024-01-24 12:46:36,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,367] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ea15946-78ca-4e37-a49e-b733d8b8f2ae/GCF_007786445.1_ASM778644v1_genomic.fna.gz | prodigal -d GCF_007786445.1_ASM778644v1_genomic.fna/cds.fna -a GCF_007786445.1_ASM778644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:56,338] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:56,339] [INFO] Task started: HMMsearch
[2024-01-24 12:46:56,339] [INFO] Running command: hmmsearch --tblout GCF_007786445.1_ASM778644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference/reference_markers.hmm GCF_007786445.1_ASM778644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:56,611] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:56,613] [INFO] Found 6/6 markers.
[2024-01-24 12:46:56,668] [INFO] Query marker FASTA was written to GCF_007786445.1_ASM778644v1_genomic.fna/markers.fasta
[2024-01-24 12:46:56,669] [INFO] Task started: Blastn
[2024-01-24 12:46:56,669] [INFO] Running command: blastn -query GCF_007786445.1_ASM778644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference/reference_markers.fasta -out GCF_007786445.1_ASM778644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:57,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:57,229] [INFO] Selected 23 target genomes.
[2024-01-24 12:46:57,229] [INFO] Target genome list was writen to GCF_007786445.1_ASM778644v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:57,233] [INFO] Task started: fastANI
[2024-01-24 12:46:57,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea15946-78ca-4e37-a49e-b733d8b8f2ae/GCF_007786445.1_ASM778644v1_genomic.fna.gz --refList GCF_007786445.1_ASM778644v1_genomic.fna/target_genomes.txt --output GCF_007786445.1_ASM778644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:20,743] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:20,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:20,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:20,760] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:47:20,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:47:20,761] [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 allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	78.928	581	2448	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	78.4574	429	2448	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	78.3418	437	2448	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	78.3285	467	2448	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	78.3252	401	2448	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	78.0386	343	2448	95	below_threshold
Paenibacillus naphthalenovorans	strain=PR-N1	GCA_900099895.1	162209	162209	type	True	77.8622	315	2448	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	77.6442	315	2448	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	77.6016	331	2448	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.1416	175	2448	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.139	317	2448	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	77.1331	342	2448	95	below_threshold
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	76.7732	105	2448	95	below_threshold
Paenibacillus swuensis	strain=DY6	GCA_001644605.1	1178515	1178515	type	True	76.6982	77	2448	95	below_threshold
Paenibacillus marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	76.6944	158	2448	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.4837	145	2448	95	below_threshold
Gorillibacterium massiliense	strain=G5	GCA_000455485.2	1280390	1280390	type	True	76.4789	83	2448	95	below_threshold
Paenibacillus antri	strain=SYSU K30003	GCA_005765165.1	2582848	2582848	type	True	76.4301	152	2448	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.394	118	2448	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.3596	190	2448	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.2201	118	2448	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.1128	116	2448	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	76.0798	130	2448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:20,762] [INFO] DFAST Taxonomy check result was written to GCF_007786445.1_ASM778644v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:20,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:20,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:20,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference/checkm_data
[2024-01-24 12:47:20,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:20,831] [INFO] Task started: CheckM
[2024-01-24 12:47:20,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007786445.1_ASM778644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007786445.1_ASM778644v1_genomic.fna/checkm_input GCF_007786445.1_ASM778644v1_genomic.fna/checkm_result
[2024-01-24 12:48:18,776] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:18,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:18,808] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:18,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:18,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007786445.1_ASM778644v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:18,809] [INFO] Task started: Blastn
[2024-01-24 12:48:18,809] [INFO] Running command: blastn -query GCF_007786445.1_ASM778644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb88722c1-d001-4f07-8f97-902f24cae837/dqc_reference/reference_markers_gtdb.fasta -out GCF_007786445.1_ASM778644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:19,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:19,572] [INFO] Selected 19 target genomes.
[2024-01-24 12:48:19,572] [INFO] Target genome list was writen to GCF_007786445.1_ASM778644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:19,581] [INFO] Task started: fastANI
[2024-01-24 12:48:19,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea15946-78ca-4e37-a49e-b733d8b8f2ae/GCF_007786445.1_ASM778644v1_genomic.fna.gz --refList GCF_007786445.1_ASM778644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007786445.1_ASM778644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:43,201] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:43,219] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:43,219] [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_007786445.1	s__Paenibacillus_G sp007786445	100.0	2440	2448	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	conclusive
GCF_910594985.1	s__Paenibacillus_G sp910594985	78.9251	581	2448	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_910593845.1	s__Paenibacillus_G solanacearum	78.7799	597	2448	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_000722545.1	s__Paenibacillus_G tyrfis	78.468	431	2448	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	-
GCF_004000865.1	s__Paenibacillus_G elgii	78.3471	437	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	97.83	95.93	0.93	0.85	6	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	78.3332	427	2448	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_018998565.1	s__Paenibacillus_G sp018998565	78.3271	425	2448	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_900100345.1	s__Paenibacillus_G tianmuensis	78.3229	401	2448	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_004000785.1	s__Paenibacillus_G ehimensis	78.3173	469	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.10	99.10	0.93	0.93	2	-
GCF_004000985.1	s__Paenibacillus_G validus	78.0254	345	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.29	99.15	0.90	0.89	6	-
GCF_017833255.1	s__Paenibacillus_G sp017833255	78.0052	310	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900099895.1	s__Paenibacillus_G naphthalenovorans	77.8621	315	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	99.27	98.99	0.91	0.86	5	-
GCF_000250655.1	s__Paenibacillus_G mucilaginosus	77.7969	402	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.86	98.79	0.96	0.95	3	-
GCF_002234615.1	s__Paenibacillus_S rigui	77.5733	334	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012935325.2	s__Paenibacillus_C sp012935325	76.953	140	2448	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_014640555.1	s__Paenibacillus_E marchantiophytorum	76.6734	157	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004764705.1	s__R196 sp004764705	76.5086	226	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__R196	95.0	95.77	95.77	0.86	0.86	2	-
GCF_003112455.1	s__Paenibacillus_C agaridevorans	76.4561	123	2448	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_003591485.1	s__Paenibacillus_C sp003591485	76.433	112	2448	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:43,223] [INFO] GTDB search result was written to GCF_007786445.1_ASM778644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:43,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:43,227] [INFO] DFAST_QC result json was written to GCF_007786445.1_ASM778644v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:43,228] [INFO] DFAST_QC completed!
[2024-01-24 12:48:43,228] [INFO] Total running time: 0h2m8s