[2024-01-24 13:57:31,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,553] [INFO] DQC Reference Directory: /var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference
[2024-01-24 13:57:32,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:32,966] [INFO] Task started: Prodigal
[2024-01-24 13:57:32,967] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4f8c65c-0028-4861-9e56-f1ed985b0165/GCF_004354045.1_ASM435404v1_genomic.fna.gz | prodigal -d GCF_004354045.1_ASM435404v1_genomic.fna/cds.fna -a GCF_004354045.1_ASM435404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:54,695] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:54,695] [INFO] Task started: HMMsearch
[2024-01-24 13:57:54,695] [INFO] Running command: hmmsearch --tblout GCF_004354045.1_ASM435404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference/reference_markers.hmm GCF_004354045.1_ASM435404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:55,022] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:55,023] [INFO] Found 6/6 markers.
[2024-01-24 13:57:55,081] [INFO] Query marker FASTA was written to GCF_004354045.1_ASM435404v1_genomic.fna/markers.fasta
[2024-01-24 13:57:55,081] [INFO] Task started: Blastn
[2024-01-24 13:57:55,081] [INFO] Running command: blastn -query GCF_004354045.1_ASM435404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference/reference_markers.fasta -out GCF_004354045.1_ASM435404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:55,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:55,678] [INFO] Selected 21 target genomes.
[2024-01-24 13:57:55,678] [INFO] Target genome list was writen to GCF_004354045.1_ASM435404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:55,686] [INFO] Task started: fastANI
[2024-01-24 13:57:55,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f8c65c-0028-4861-9e56-f1ed985b0165/GCF_004354045.1_ASM435404v1_genomic.fna.gz --refList GCF_004354045.1_ASM435404v1_genomic.fna/target_genomes.txt --output GCF_004354045.1_ASM435404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:23,838] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:23,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:23,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:23,856] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:23,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:23,857] [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 piri	strain=MS74	GCA_004354045.1	2547395	2547395	type	True	100.0	2628	2629	95	conclusive
Paenibacillus foliorum	strain=LMG 31456	GCA_013141765.1	2654974	2654974	type	True	79.0935	673	2629	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	78.6656	593	2629	95	below_threshold
Paenibacillus rigui	strain=JCM 16352	GCA_002234615.1	554312	554312	type	True	78.4588	495	2629	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	78.1532	453	2629	95	below_threshold
Paenibacillus tyrfis	strain=MSt1	GCA_000722545.1	1501230	1501230	type	True	77.8445	382	2629	95	below_threshold
Paenibacillus xerothermodurans	strain=ATCC 27380	GCA_002220865.2	1977292	1977292	type	True	77.7567	289	2629	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	77.7563	369	2629	95	below_threshold
Paenibacillus puerhi	strain=SJY2	GCA_009846885.1	2692622	2692622	type	True	77.6793	274	2629	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	77.6428	339	2629	95	below_threshold
Paenibacillus ehimensis	strain=NBRC 15659	GCA_004000785.1	79264	79264	type	True	77.5117	370	2629	95	below_threshold
Paenibacillus validus	strain=NBRC 15382	GCA_004000985.1	44253	44253	type	True	77.3865	293	2629	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	77.0541	326	2629	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	77.0201	205	2629	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	76.9044	274	2629	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.8831	150	2629	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.5776	207	2629	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	76.5695	174	2629	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.393	126	2629	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	76.3753	105	2629	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	76.0037	117	2629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,858] [INFO] DFAST Taxonomy check result was written to GCF_004354045.1_ASM435404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:23,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:23,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:23,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference/checkm_data
[2024-01-24 13:58:23,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:23,934] [INFO] Task started: CheckM
[2024-01-24 13:58:23,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354045.1_ASM435404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354045.1_ASM435404v1_genomic.fna/checkm_input GCF_004354045.1_ASM435404v1_genomic.fna/checkm_result
[2024-01-24 13:59:25,704] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:25,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,735] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:25,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:25,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354045.1_ASM435404v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:25,736] [INFO] Task started: Blastn
[2024-01-24 13:59:25,736] [INFO] Running command: blastn -query GCF_004354045.1_ASM435404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf429e994-5347-404a-b12d-50f48cba24f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354045.1_ASM435404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:26,647] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:26,651] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:26,651] [INFO] Target genome list was writen to GCF_004354045.1_ASM435404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:26,682] [INFO] Task started: fastANI
[2024-01-24 13:59:26,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4f8c65c-0028-4861-9e56-f1ed985b0165/GCF_004354045.1_ASM435404v1_genomic.fna.gz --refList GCF_004354045.1_ASM435404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354045.1_ASM435404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:52,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:52,340] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:52,341] [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_004354045.1	s__Paenibacillus_S piri	100.0	2628	2629	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	conclusive
GCF_013141765.1	s__Paenibacillus_S foliorum	79.1011	672	2629	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_002042965.1	s__Paenibacillus_S sp002042965	78.7487	482	2629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	97.63	97.63	0.93	0.93	2	-
GCF_002234615.1	s__Paenibacillus_S rigui	78.4666	494	2629	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_000686845.1	s__Paenibacillus_S sp000686845	78.2959	392	2629	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_910594985.1	s__Paenibacillus_G sp910594985	78.1566	450	2629	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	77.9667	429	2629	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	77.9658	390	2629	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	77.8513	380	2629	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	77.7626	367	2629	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_004307995.1	s__Paenibacillus_AF thalictri	77.7531	434	2629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002220865.2	s__Paenibacillus_S xerothermodurans	77.7457	290	2629	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_001399685.1	s__Paenibacillus_G sp001399685	77.745	360	2629	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_009846885.1	s__Paenibacillus_G puerhi	77.6793	274	2629	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	77.5361	367	2629	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	77.3865	293	2629	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_003217775.1	s__Paenibacillus_AB flagellatus	76.9042	272	2629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365285.1	s__Paenibacillus_Z rhizovicinus	76.5816	171	2629	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_002205895.1	s__Saccharibacillus sp002205895	76.2052	92	2629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:52,343] [INFO] GTDB search result was written to GCF_004354045.1_ASM435404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:52,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:52,349] [INFO] DFAST_QC result json was written to GCF_004354045.1_ASM435404v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:52,350] [INFO] DFAST_QC completed!
[2024-01-24 13:59:52,350] [INFO] Total running time: 0h2m21s