[2024-01-24 15:26:04,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,024] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg56dc7b2b-7898-4d80-9b51-3b25a15b3c5e/GCF_014192105.1_ASM1419210v1_genomic.fna.gz | prodigal -d GCF_014192105.1_ASM1419210v1_genomic.fna/cds.fna -a GCF_014192105.1_ASM1419210v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:28,603] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:28,604] [INFO] Task started: HMMsearch
[2024-01-24 15:26:28,604] [INFO] Running command: hmmsearch --tblout GCF_014192105.1_ASM1419210v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference/reference_markers.hmm GCF_014192105.1_ASM1419210v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:29,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:29,009] [INFO] Found 6/6 markers.
[2024-01-24 15:26:29,076] [INFO] Query marker FASTA was written to GCF_014192105.1_ASM1419210v1_genomic.fna/markers.fasta
[2024-01-24 15:26:29,077] [INFO] Task started: Blastn
[2024-01-24 15:26:29,077] [INFO] Running command: blastn -query GCF_014192105.1_ASM1419210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference/reference_markers.fasta -out GCF_014192105.1_ASM1419210v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:29,691] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:29,695] [INFO] Selected 18 target genomes.
[2024-01-24 15:26:29,695] [INFO] Target genome list was writen to GCF_014192105.1_ASM1419210v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:29,704] [INFO] Task started: fastANI
[2024-01-24 15:26:29,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg56dc7b2b-7898-4d80-9b51-3b25a15b3c5e/GCF_014192105.1_ASM1419210v1_genomic.fna.gz --refList GCF_014192105.1_ASM1419210v1_genomic.fna/target_genomes.txt --output GCF_014192105.1_ASM1419210v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:51,365] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:51,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:51,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:51,391] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:51,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:51,391] [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 phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	100.0	2599	2604	95	conclusive
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	79.853	992	2604	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.9354	474	2604	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	77.8345	430	2604	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_009909195.1	742054	742054	type	True	77.7842	418	2604	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.7331	353	2604	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.6829	450	2604	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	77.6682	361	2604	95	below_threshold
Paenibacillus sacheonensis	strain=DSM 23054	GCA_016908255.1	742054	742054	type	True	77.6207	418	2604	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	77.4672	282	2604	95	below_threshold
Paenibacillus baekrokdamisoli	strain=KCTC 33723	GCA_003945345.1	1712516	1712516	type	True	77.2919	191	2604	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	77.2257	217	2604	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.1587	196	2604	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.1154	216	2604	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	77.0066	328	2604	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	76.7682	275	2604	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	76.6687	124	2604	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.528	136	2604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:51,393] [INFO] DFAST Taxonomy check result was written to GCF_014192105.1_ASM1419210v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:51,394] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:51,394] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:51,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference/checkm_data
[2024-01-24 15:26:51,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:51,499] [INFO] Task started: CheckM
[2024-01-24 15:26:51,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192105.1_ASM1419210v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192105.1_ASM1419210v1_genomic.fna/checkm_input GCF_014192105.1_ASM1419210v1_genomic.fna/checkm_result
[2024-01-24 15:27:53,553] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:53,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:53,581] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:53,581] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:53,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192105.1_ASM1419210v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:53,582] [INFO] Task started: Blastn
[2024-01-24 15:27:53,582] [INFO] Running command: blastn -query GCF_014192105.1_ASM1419210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dba8b80-e1bf-45d9-afcb-a1c03d258dad/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192105.1_ASM1419210v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,406] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,412] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:54,413] [INFO] Target genome list was writen to GCF_014192105.1_ASM1419210v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:54,424] [INFO] Task started: fastANI
[2024-01-24 15:27:54,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg56dc7b2b-7898-4d80-9b51-3b25a15b3c5e/GCF_014192105.1_ASM1419210v1_genomic.fna.gz --refList GCF_014192105.1_ASM1419210v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192105.1_ASM1419210v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:12,004] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:12,017] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:12,017] [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_014192105.1	s__Paenibacillus_Z phyllosphaerae	100.0	2599	2604	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008124765.1	s__Paenibacillus_Z methanolicus	79.8498	990	2604	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	77.9567	356	2604	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_010119935.1	s__Paenibacillus_Z lycopersici	77.9279	475	2604	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_003386535.1	s__Paenibacillus_Z taihuensis	77.8633	383	2604	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_010365285.1	s__Paenibacillus_Z rhizovicinus	77.8527	427	2604	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	77.7553	417	2604	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_016908135.1	s__Paenibacillus_Z mendelii	77.7011	360	2604	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_900113915.1	s__Paenibacillus_Z sp900113915	77.6941	465	2604	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	96.39	96.39	0.86	0.86	2	-
GCF_009737085.1	s__Paenibacillus_C sp009737085	77.5143	232	2604	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_004000825.1	s__Paenibacillus_T kobensis	77.4651	282	2604	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_004345425.1	s__Paenibacillus_C sp004345425	77.3197	341	2604	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_000513275.1	s__Paenibacillus_C gorillae	77.1275	215	2604	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_000422485.1	s__Paenibacillus_O pasadenensis	77.0197	327	2604	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:12,019] [INFO] GTDB search result was written to GCF_014192105.1_ASM1419210v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:12,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:12,024] [INFO] DFAST_QC result json was written to GCF_014192105.1_ASM1419210v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:12,024] [INFO] DFAST_QC completed!
[2024-01-24 15:28:12,024] [INFO] Total running time: 0h2m7s