[2024-01-25 19:50:50,474] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:50,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:50,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference
[2024-01-25 19:50:51,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:51,636] [INFO] Task started: Prodigal
[2024-01-25 19:50:51,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cbe4b9d-dcb0-44e3-b021-51fbc6850acd/GCF_017086365.1_ASM1708636v1_genomic.fna.gz | prodigal -d GCF_017086365.1_ASM1708636v1_genomic.fna/cds.fna -a GCF_017086365.1_ASM1708636v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:05,729] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:05,730] [INFO] Task started: HMMsearch
[2024-01-25 19:51:05,730] [INFO] Running command: hmmsearch --tblout GCF_017086365.1_ASM1708636v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference/reference_markers.hmm GCF_017086365.1_ASM1708636v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:06,006] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:06,007] [INFO] Found 6/6 markers.
[2024-01-25 19:51:06,054] [INFO] Query marker FASTA was written to GCF_017086365.1_ASM1708636v1_genomic.fna/markers.fasta
[2024-01-25 19:51:06,055] [INFO] Task started: Blastn
[2024-01-25 19:51:06,055] [INFO] Running command: blastn -query GCF_017086365.1_ASM1708636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference/reference_markers.fasta -out GCF_017086365.1_ASM1708636v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:06,649] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:06,652] [INFO] Selected 19 target genomes.
[2024-01-25 19:51:06,652] [INFO] Target genome list was writen to GCF_017086365.1_ASM1708636v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:06,674] [INFO] Task started: fastANI
[2024-01-25 19:51:06,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbe4b9d-dcb0-44e3-b021-51fbc6850acd/GCF_017086365.1_ASM1708636v1_genomic.fna.gz --refList GCF_017086365.1_ASM1708636v1_genomic.fna/target_genomes.txt --output GCF_017086365.1_ASM1708636v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:33,257] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:33,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:33,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:33,269] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:33,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:33,269] [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 tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	100.0	2090	2091	95	conclusive
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	94.0874	1716	2091	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	82.8434	1324	2091	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	81.3292	1112	2091	95	below_threshold
Paenibacillus graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	81.2485	1039	2091	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	81.2345	1019	2091	95	below_threshold
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	81.1809	1023	2091	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	81.1242	1053	2091	95	below_threshold
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	81.0875	1050	2091	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	81.0674	1081	2091	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	81.0585	871	2091	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	80.921	788	2091	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	80.591	982	2091	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	80.0178	887	2091	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.6255	583	2091	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.1457	483	2091	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	77.1667	216	2091	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	76.9912	151	2091	95	below_threshold
Paenibacillus polysaccharolyticus	strain=BL9	GCA_900102085.1	582692	582692	type	True	76.9618	133	2091	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:33,270] [INFO] DFAST Taxonomy check result was written to GCF_017086365.1_ASM1708636v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:33,271] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:33,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:33,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference/checkm_data
[2024-01-25 19:51:33,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:33,332] [INFO] Task started: CheckM
[2024-01-25 19:51:33,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017086365.1_ASM1708636v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017086365.1_ASM1708636v1_genomic.fna/checkm_input GCF_017086365.1_ASM1708636v1_genomic.fna/checkm_result
[2024-01-25 19:52:15,524] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:15,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:15,542] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:15,542] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:15,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017086365.1_ASM1708636v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:15,543] [INFO] Task started: Blastn
[2024-01-25 19:52:15,544] [INFO] Running command: blastn -query GCF_017086365.1_ASM1708636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68a1eb38-b390-4cf6-9c82-033fa7b88c05/dqc_reference/reference_markers_gtdb.fasta -out GCF_017086365.1_ASM1708636v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:16,394] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:16,397] [INFO] Selected 15 target genomes.
[2024-01-25 19:52:16,397] [INFO] Target genome list was writen to GCF_017086365.1_ASM1708636v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:16,410] [INFO] Task started: fastANI
[2024-01-25 19:52:16,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cbe4b9d-dcb0-44e3-b021-51fbc6850acd/GCF_017086365.1_ASM1708636v1_genomic.fna.gz --refList GCF_017086365.1_ASM1708636v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017086365.1_ASM1708636v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:39,393] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:39,402] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:39,402] [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_017086365.1	s__Paenibacillus sp017086365	100.0	2090	2091	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_001368795.1	s__Paenibacillus ihuae	94.0903	1715	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001517085.1	s__Paenibacillus sp001517085	82.9513	1323	2091	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	82.8422	1325	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
GCF_000758625.1	s__Paenibacillus sp000758625	82.7558	1230	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000723885.1	s__Paenibacillus camerounensis	82.297	1188	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.67	95.67	0.88	0.88	2	-
GCF_000758525.1	s__Paenibacillus sp000758525	82.0556	1201	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_000758665.1	s__Paenibacillus borealis	81.3178	1111	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758705.1	s__Paenibacillus graminis	81.2541	1038	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000758605.1	s__Paenibacillus sp000758605	81.1986	1156	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102965.1	s__Paenibacillus jilunlii	81.185	1023	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_013141775.1	s__Paenibacillus phytohabitans	81.0829	1078	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_003060825.1	s__Paenibacillus_A sp003060825	78.8	154	2091	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_014639235.1	s__Paenibacillus silvae	77.0184	152	2091	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_018998565.1	s__Paenibacillus_G sp018998565	76.0548	93	2091	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	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:39,404] [INFO] GTDB search result was written to GCF_017086365.1_ASM1708636v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:39,404] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:39,407] [INFO] DFAST_QC result json was written to GCF_017086365.1_ASM1708636v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:39,407] [INFO] DFAST_QC completed!
[2024-01-25 19:52:39,408] [INFO] Total running time: 0h1m49s