[2024-01-24 12:06:13,499] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference
[2024-01-24 12:06:14,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,910] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dfb8895-3ce3-4669-8771-e02700246adf/GCF_024498075.1_ASM2449807v1_genomic.fna.gz | prodigal -d GCF_024498075.1_ASM2449807v1_genomic.fna/cds.fna -a GCF_024498075.1_ASM2449807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:37,035] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:37,035] [INFO] Task started: HMMsearch
[2024-01-24 12:06:37,035] [INFO] Running command: hmmsearch --tblout GCF_024498075.1_ASM2449807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference/reference_markers.hmm GCF_024498075.1_ASM2449807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:37,573] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:37,574] [INFO] Found 6/6 markers.
[2024-01-24 12:06:37,647] [INFO] Query marker FASTA was written to GCF_024498075.1_ASM2449807v1_genomic.fna/markers.fasta
[2024-01-24 12:06:37,647] [INFO] Task started: Blastn
[2024-01-24 12:06:37,647] [INFO] Running command: blastn -query GCF_024498075.1_ASM2449807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference/reference_markers.fasta -out GCF_024498075.1_ASM2449807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,324] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,327] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:38,328] [INFO] Target genome list was writen to GCF_024498075.1_ASM2449807v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:38,332] [INFO] Task started: fastANI
[2024-01-24 12:06:38,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dfb8895-3ce3-4669-8771-e02700246adf/GCF_024498075.1_ASM2449807v1_genomic.fna.gz --refList GCF_024498075.1_ASM2449807v1_genomic.fna/target_genomes.txt --output GCF_024498075.1_ASM2449807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:58,442] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:58,442] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:58,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:58,457] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:58,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:58,457] [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 mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	100.0	2672	2673	95	conclusive
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	77.9323	323	2673	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	77.8322	338	2673	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.7805	288	2673	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.6224	315	2673	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.5379	317	2673	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.5112	274	2673	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.4693	301	2673	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	77.4243	292	2673	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.4221	326	2673	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	77.4011	309	2673	95	below_threshold
Paenibacillus beijingensis	strain=DSM 24997	GCA_000961095.1	1126833	1126833	type	True	77.2284	208	2673	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.0693	196	2673	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	76.8469	181	2673	95	below_threshold
Paenibacillus radicis	strain=CGMCC 1.15286	GCA_014641555.1	1737354	1737354	type	True	76.7775	201	2673	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.7197	80	2673	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.2654	148	2673	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:58,459] [INFO] DFAST Taxonomy check result was written to GCF_024498075.1_ASM2449807v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:58,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:58,460] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:58,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference/checkm_data
[2024-01-24 12:06:58,461] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:58,538] [INFO] Task started: CheckM
[2024-01-24 12:06:58,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498075.1_ASM2449807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498075.1_ASM2449807v1_genomic.fna/checkm_input GCF_024498075.1_ASM2449807v1_genomic.fna/checkm_result
[2024-01-24 12:08:01,324] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:01,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:01,357] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:01,358] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:01,358] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498075.1_ASM2449807v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:01,359] [INFO] Task started: Blastn
[2024-01-24 12:08:01,359] [INFO] Running command: blastn -query GCF_024498075.1_ASM2449807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c16d21b-8b87-4dc4-b3af-14e62a1d30f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498075.1_ASM2449807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:02,159] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:02,164] [INFO] Selected 15 target genomes.
[2024-01-24 12:08:02,164] [INFO] Target genome list was writen to GCF_024498075.1_ASM2449807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:02,171] [INFO] Task started: fastANI
[2024-01-24 12:08:02,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dfb8895-3ce3-4669-8771-e02700246adf/GCF_024498075.1_ASM2449807v1_genomic.fna.gz --refList GCF_024498075.1_ASM2449807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498075.1_ASM2449807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:19,007] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:19,026] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:19,026] [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_016908135.1	s__Paenibacillus_Z mendelii	99.9949	2666	2673	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_014192105.1	s__Paenibacillus_Z phyllosphaerae	77.8343	339	2673	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_900116125.1	s__Paenibacillus_Z sp900116125	77.769	289	2673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	77.612	316	2673	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	77.5989	337	2673	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_003268025.1	s__Paenibacillus_Z montanisoli	77.5378	317	2673	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_003952225.1	s__Paenibacillus_Z albus	77.523	276	2673	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_900110075.1	s__Paenibacillus_Z sp900110075	77.4437	240	2673	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	77.4221	326	2673	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	77.4145	293	2673	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	77.4098	309	2673	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	77.4083	284	2673	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_000961095.1	s__Paenibacillus_O beijingensis	77.2288	207	2673	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513275.1	s__Paenibacillus_C gorillae	76.8469	181	2673	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_014641555.1	s__Paenibacillus_C radicis	76.7775	201	2673	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 12:08:19,028] [INFO] GTDB search result was written to GCF_024498075.1_ASM2449807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:19,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:19,033] [INFO] DFAST_QC result json was written to GCF_024498075.1_ASM2449807v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:19,033] [INFO] DFAST_QC completed!
[2024-01-24 12:08:19,033] [INFO] Total running time: 0h2m6s