[2024-01-24 15:26:53,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:53,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:53,548] [INFO] DQC Reference Directory: /var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference
[2024-01-24 15:26:54,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:54,832] [INFO] Task started: Prodigal
[2024-01-24 15:26:54,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg8386376a-910b-4eec-8b7c-21b561b68f5a/GCF_014947195.2_ASM1494719v2_genomic.fna.gz | prodigal -d GCF_014947195.2_ASM1494719v2_genomic.fna/cds.fna -a GCF_014947195.2_ASM1494719v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,841] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,841] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,842] [INFO] Running command: hmmsearch --tblout GCF_014947195.2_ASM1494719v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference/reference_markers.hmm GCF_014947195.2_ASM1494719v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:09,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:09,103] [INFO] Found 6/6 markers.
[2024-01-24 15:27:09,144] [INFO] Query marker FASTA was written to GCF_014947195.2_ASM1494719v2_genomic.fna/markers.fasta
[2024-01-24 15:27:09,144] [INFO] Task started: Blastn
[2024-01-24 15:27:09,144] [INFO] Running command: blastn -query GCF_014947195.2_ASM1494719v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference/reference_markers.fasta -out GCF_014947195.2_ASM1494719v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:09,748] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:09,752] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:09,752] [INFO] Target genome list was writen to GCF_014947195.2_ASM1494719v2_genomic.fna/target_genomes.txt
[2024-01-24 15:27:09,756] [INFO] Task started: fastANI
[2024-01-24 15:27:09,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg8386376a-910b-4eec-8b7c-21b561b68f5a/GCF_014947195.2_ASM1494719v2_genomic.fna.gz --refList GCF_014947195.2_ASM1494719v2_genomic.fna/target_genomes.txt --output GCF_014947195.2_ASM1494719v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:20,183] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:20,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:20,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:20,196] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:20,200] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:20,202] [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 timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	87.8464	1313	1638	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	85.6312	1331	1638	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	85.4361	1226	1638	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	82.9309	1089	1638	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	79.6644	716	1638	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	79.4342	715	1638	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.1286	153	1638	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.4535	110	1638	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.2984	164	1638	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:20,203] [INFO] DFAST Taxonomy check result was written to GCF_014947195.2_ASM1494719v2_genomic.fna/tc_result.tsv
[2024-01-24 15:27:20,204] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:20,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:20,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference/checkm_data
[2024-01-24 15:27:20,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:20,252] [INFO] Task started: CheckM
[2024-01-24 15:27:20,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014947195.2_ASM1494719v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014947195.2_ASM1494719v2_genomic.fna/checkm_input GCF_014947195.2_ASM1494719v2_genomic.fna/checkm_result
[2024-01-24 15:28:03,505] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:03,507] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:03,526] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:03,527] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:03,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014947195.2_ASM1494719v2_genomic.fna/markers.fasta)
[2024-01-24 15:28:03,527] [INFO] Task started: Blastn
[2024-01-24 15:28:03,527] [INFO] Running command: blastn -query GCF_014947195.2_ASM1494719v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga3acef4b-d6a7-46b5-a58f-8809e1e7c912/dqc_reference/reference_markers_gtdb.fasta -out GCF_014947195.2_ASM1494719v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:04,332] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:04,338] [INFO] Selected 5 target genomes.
[2024-01-24 15:28:04,338] [INFO] Target genome list was writen to GCF_014947195.2_ASM1494719v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:04,342] [INFO] Task started: fastANI
[2024-01-24 15:28:04,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg8386376a-910b-4eec-8b7c-21b561b68f5a/GCF_014947195.2_ASM1494719v2_genomic.fna.gz --refList GCF_014947195.2_ASM1494719v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014947195.2_ASM1494719v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:10,778] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:10,784] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:10,784] [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_009725205.1	s__Paenibacillus_A timonensis	98.1381	1504	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	conclusive
GCA_900766135.1	s__Paenibacillus_A sp900766135	87.4589	1330	1638	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_001486505.1	s__Paenibacillus_A rubinfantis	85.6312	1331	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900021165.1	s__Paenibacillus_A phocaensis	85.4398	1225	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000159955.1	s__Paenibacillus_A sp000159955	83.8159	1156	1638	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:10,786] [INFO] GTDB search result was written to GCF_014947195.2_ASM1494719v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:10,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:10,789] [INFO] DFAST_QC result json was written to GCF_014947195.2_ASM1494719v2_genomic.fna/dqc_result.json
[2024-01-24 15:28:10,790] [INFO] DFAST_QC completed!
[2024-01-24 15:28:10,790] [INFO] Total running time: 0h1m17s