[2024-01-24 12:31:51,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,178] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,178] [INFO] DQC Reference Directory: /var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference
[2024-01-24 12:31:52,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,427] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,428] [INFO] Running command: gunzip -c /var/lib/cwl/stga68f31e4-65b3-4298-b40b-d13f70df38f0/GCF_022427145.1_ASM2242714v1_genomic.fna.gz | prodigal -d GCF_022427145.1_ASM2242714v1_genomic.fna/cds.fna -a GCF_022427145.1_ASM2242714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:06,549] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:06,550] [INFO] Task started: HMMsearch
[2024-01-24 12:32:06,550] [INFO] Running command: hmmsearch --tblout GCF_022427145.1_ASM2242714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference/reference_markers.hmm GCF_022427145.1_ASM2242714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:06,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:06,853] [INFO] Found 6/6 markers.
[2024-01-24 12:32:06,904] [INFO] Query marker FASTA was written to GCF_022427145.1_ASM2242714v1_genomic.fna/markers.fasta
[2024-01-24 12:32:06,905] [INFO] Task started: Blastn
[2024-01-24 12:32:06,905] [INFO] Running command: blastn -query GCF_022427145.1_ASM2242714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference/reference_markers.fasta -out GCF_022427145.1_ASM2242714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:07,520] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:07,525] [INFO] Selected 9 target genomes.
[2024-01-24 12:32:07,526] [INFO] Target genome list was writen to GCF_022427145.1_ASM2242714v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:07,533] [INFO] Task started: fastANI
[2024-01-24 12:32:07,534] [INFO] Running command: fastANI --query /var/lib/cwl/stga68f31e4-65b3-4298-b40b-d13f70df38f0/GCF_022427145.1_ASM2242714v1_genomic.fna.gz --refList GCF_022427145.1_ASM2242714v1_genomic.fna/target_genomes.txt --output GCF_022427145.1_ASM2242714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:17,562] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:17,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:17,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:17,572] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:17,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:17,572] [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	100.0	1674	1681	95	conclusive
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	87.6936	1316	1681	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	87.0077	1234	1681	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	84.1961	1137	1681	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	80.2373	823	1681	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	80.0919	800	1681	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.805	319	1681	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.474	241	1681	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.9151	109	1681	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:17,574] [INFO] DFAST Taxonomy check result was written to GCF_022427145.1_ASM2242714v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:17,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:17,575] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:17,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference/checkm_data
[2024-01-24 12:32:17,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:17,627] [INFO] Task started: CheckM
[2024-01-24 12:32:17,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022427145.1_ASM2242714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022427145.1_ASM2242714v1_genomic.fna/checkm_input GCF_022427145.1_ASM2242714v1_genomic.fna/checkm_result
[2024-01-24 12:33:00,299] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:00,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:00,327] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:00,328] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:00,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022427145.1_ASM2242714v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:00,329] [INFO] Task started: Blastn
[2024-01-24 12:33:00,329] [INFO] Running command: blastn -query GCF_022427145.1_ASM2242714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6e20554-4d61-4b25-ae84-baacf313f4be/dqc_reference/reference_markers_gtdb.fasta -out GCF_022427145.1_ASM2242714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:01,122] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:01,126] [INFO] Selected 5 target genomes.
[2024-01-24 12:33:01,126] [INFO] Target genome list was writen to GCF_022427145.1_ASM2242714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:01,131] [INFO] Task started: fastANI
[2024-01-24 12:33:01,131] [INFO] Running command: fastANI --query /var/lib/cwl/stga68f31e4-65b3-4298-b40b-d13f70df38f0/GCF_022427145.1_ASM2242714v1_genomic.fna.gz --refList GCF_022427145.1_ASM2242714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022427145.1_ASM2242714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:07,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:07,646] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:33:07,646] [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
GCA_900766135.1	s__Paenibacillus_A sp900766135	93.135	1421	1681	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_009725205.1	s__Paenibacillus_A timonensis	87.8136	1329	1681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	87.6753	1318	1681	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	87.0218	1231	1681	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	85.4141	1176	1681	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 12:33:07,648] [INFO] GTDB search result was written to GCF_022427145.1_ASM2242714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:07,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:07,653] [INFO] DFAST_QC result json was written to GCF_022427145.1_ASM2242714v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:07,653] [INFO] DFAST_QC completed!
[2024-01-24 12:33:07,653] [INFO] Total running time: 0h1m16s