[2024-01-24 13:46:01,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,207] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference
[2024-01-24 13:46:02,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,523] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ac3c5f2-7f35-4172-b63a-e421240cfcd9/GCF_008973665.1_ASM897366v1_genomic.fna.gz | prodigal -d GCF_008973665.1_ASM897366v1_genomic.fna/cds.fna -a GCF_008973665.1_ASM897366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:19,452] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:19,453] [INFO] Task started: HMMsearch
[2024-01-24 13:46:19,453] [INFO] Running command: hmmsearch --tblout GCF_008973665.1_ASM897366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference/reference_markers.hmm GCF_008973665.1_ASM897366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:19,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:19,768] [INFO] Found 6/6 markers.
[2024-01-24 13:46:19,825] [INFO] Query marker FASTA was written to GCF_008973665.1_ASM897366v1_genomic.fna/markers.fasta
[2024-01-24 13:46:19,826] [INFO] Task started: Blastn
[2024-01-24 13:46:19,826] [INFO] Running command: blastn -query GCF_008973665.1_ASM897366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference/reference_markers.fasta -out GCF_008973665.1_ASM897366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:20,461] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:20,465] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:20,466] [INFO] Target genome list was writen to GCF_008973665.1_ASM897366v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:20,476] [INFO] Task started: fastANI
[2024-01-24 13:46:20,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac3c5f2-7f35-4172-b63a-e421240cfcd9/GCF_008973665.1_ASM897366v1_genomic.fna.gz --refList GCF_008973665.1_ASM897366v1_genomic.fna/target_genomes.txt --output GCF_008973665.1_ASM897366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:42,273] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:42,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:42,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:42,290] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:42,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:42,291] [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 tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	100.0	2106	2107	95	conclusive
Paenibacillus tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	86.2196	1681	2107	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	79.6336	943	2107	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	79.5427	873	2107	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	79.5068	857	2107	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	79.4956	939	2107	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.494	841	2107	95	below_threshold
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	79.4084	719	2107	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	79.3508	913	2107	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	79.3348	887	2107	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	79.2676	731	2107	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	79.2513	862	2107	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	79.2487	873	2107	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	78.6511	479	2107	95	below_threshold
Paenibacillus sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	78.3854	459	2107	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.323	499	2107	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	78.2922	460	2107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:42,292] [INFO] DFAST Taxonomy check result was written to GCF_008973665.1_ASM897366v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:42,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:42,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:42,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference/checkm_data
[2024-01-24 13:46:42,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:42,354] [INFO] Task started: CheckM
[2024-01-24 13:46:42,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008973665.1_ASM897366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008973665.1_ASM897366v1_genomic.fna/checkm_input GCF_008973665.1_ASM897366v1_genomic.fna/checkm_result
[2024-01-24 13:47:32,337] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:32,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:32,385] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:32,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:32,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008973665.1_ASM897366v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:32,387] [INFO] Task started: Blastn
[2024-01-24 13:47:32,387] [INFO] Running command: blastn -query GCF_008973665.1_ASM897366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e3df3e1-2e62-4373-93d0-add410a3bc9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008973665.1_ASM897366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:33,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:33,283] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:33,283] [INFO] Target genome list was writen to GCF_008973665.1_ASM897366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:33,364] [INFO] Task started: fastANI
[2024-01-24 13:47:33,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ac3c5f2-7f35-4172-b63a-e421240cfcd9/GCF_008973665.1_ASM897366v1_genomic.fna.gz --refList GCF_008973665.1_ASM897366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008973665.1_ASM897366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:57,435] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:57,450] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:57,450] [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_008973665.1	s__Paenibacillus tengchongensis	100.0	2106	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008635795.1	s__Paenibacillus tepidiphilus	86.2245	1680	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099765.1	s__Paenibacillus typhae	79.6554	940	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
GCF_000758525.1	s__Paenibacillus sp000758525	79.5447	897	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_001517085.1	s__Paenibacillus sp001517085	79.5443	943	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758625.1	s__Paenibacillus sp000758625	79.5199	977	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017086365.1	s__Paenibacillus sp017086365	79.511	839	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758665.1	s__Paenibacillus borealis	79.4844	943	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772475.1	s__Paenibacillus sonchi	79.4844	861	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	99.97	99.97	1.00	1.00	2	-
GCF_900111565.1	s__Paenibacillus sp900111565	79.4582	795	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141775.1	s__Paenibacillus phytohabitans	79.359	911	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_000981585.1	s__Paenibacillus riograndensis	79.3238	872	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	97.36	97.36	0.91	0.91	2	-
GCF_000758605.1	s__Paenibacillus sp000758605	79.2746	902	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874735.1	s__Paenibacillus silagei	79.2346	874	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_001909055.1	s__Paenibacillus helianthi	78.8943	764	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.61	95.31	0.90	0.83	4	-
GCF_000758545.1	s__Paenibacillus sp000758545	78.4826	393	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.87	97.65	0.91	0.90	4	-
GCF_002264395.1	s__Paenibacillus sp002264395	78.4426	368	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
GCF_000993825.1	s__Paenibacillus durus_B	78.3456	466	2107	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:57,452] [INFO] GTDB search result was written to GCF_008973665.1_ASM897366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:57,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:57,457] [INFO] DFAST_QC result json was written to GCF_008973665.1_ASM897366v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:57,457] [INFO] DFAST_QC completed!
[2024-01-24 13:47:57,457] [INFO] Total running time: 0h1m56s