[2024-01-24 13:40:28,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference
[2024-01-24 13:40:29,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,527] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,528] [INFO] Running command: gunzip -c /var/lib/cwl/stge84de9ae-4f5a-436c-8567-6f661c18a92e/GCF_004001085.1_ASM400108v1_genomic.fna.gz | prodigal -d GCF_004001085.1_ASM400108v1_genomic.fna/cds.fna -a GCF_004001085.1_ASM400108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:43,890] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:43,890] [INFO] Task started: HMMsearch
[2024-01-24 13:40:43,890] [INFO] Running command: hmmsearch --tblout GCF_004001085.1_ASM400108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference/reference_markers.hmm GCF_004001085.1_ASM400108v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,272] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,322] [INFO] Query marker FASTA was written to GCF_004001085.1_ASM400108v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,322] [INFO] Task started: Blastn
[2024-01-24 13:40:44,322] [INFO] Running command: blastn -query GCF_004001085.1_ASM400108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference/reference_markers.fasta -out GCF_004001085.1_ASM400108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:45,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:45,183] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:45,183] [INFO] Target genome list was writen to GCF_004001085.1_ASM400108v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:45,189] [INFO] Task started: fastANI
[2024-01-24 13:40:45,189] [INFO] Running command: fastANI --query /var/lib/cwl/stge84de9ae-4f5a-436c-8567-6f661c18a92e/GCF_004001085.1_ASM400108v1_genomic.fna.gz --refList GCF_004001085.1_ASM400108v1_genomic.fna/target_genomes.txt --output GCF_004001085.1_ASM400108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:59,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:59,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:59,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:59,522] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:59,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:59,522] [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 pasadenensis	strain=NBRC 101214	GCA_004001085.1	217090	217090	type	True	100.0	1797	1812	95	conclusive
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	99.9853	1792	1812	95	conclusive
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	90.64	1404	1812	95	below_threshold
Paenibacillus humicus	strain=NBRC 102415	GCA_004000905.1	412861	412861	type	True	81.071	925	1812	95	below_threshold
Paenibacillus herberti	strain=R33	GCA_002233675.1	1619309	1619309	type	True	79.128	639	1812	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	78.2353	568	1812	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	77.7077	434	1812	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	77.5072	473	1812	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.7984	182	1812	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.4843	217	1812	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.2015	201	1812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:59,524] [INFO] DFAST Taxonomy check result was written to GCF_004001085.1_ASM400108v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:59,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:59,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:59,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference/checkm_data
[2024-01-24 13:40:59,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:59,584] [INFO] Task started: CheckM
[2024-01-24 13:40:59,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004001085.1_ASM400108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004001085.1_ASM400108v1_genomic.fna/checkm_input GCF_004001085.1_ASM400108v1_genomic.fna/checkm_result
[2024-01-24 13:41:43,248] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:43,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:43,266] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:43,267] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:43,267] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004001085.1_ASM400108v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:43,267] [INFO] Task started: Blastn
[2024-01-24 13:41:43,268] [INFO] Running command: blastn -query GCF_004001085.1_ASM400108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg127ae068-4efd-4d00-84c0-6f0d08fa2123/dqc_reference/reference_markers_gtdb.fasta -out GCF_004001085.1_ASM400108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:44,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:44,456] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:44,457] [INFO] Target genome list was writen to GCF_004001085.1_ASM400108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:44,462] [INFO] Task started: fastANI
[2024-01-24 13:41:44,462] [INFO] Running command: fastANI --query /var/lib/cwl/stge84de9ae-4f5a-436c-8567-6f661c18a92e/GCF_004001085.1_ASM400108v1_genomic.fna.gz --refList GCF_004001085.1_ASM400108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004001085.1_ASM400108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:54,361] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:54,369] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:54,370] [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_000422485.1	s__Paenibacillus_O pasadenensis	99.9853	1792	1812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	conclusive
GCF_012676905.1	s__Paenibacillus_O sp012676905	90.6625	1402	1812	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_004000905.1	s__Paenibacillus_O humicus	81.0583	926	1812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	98.90	98.81	0.93	0.93	3	-
GCF_002243345.2	s__Paenibacillus_O sp002243345	80.898	936	1812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.98	99.98	0.98	0.98	4	-
GCF_002233675.1	s__Paenibacillus_O herberti	79.1145	641	1812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900105225.1	s__Paenibacillus_O sp900105225	79.0791	626	1812	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_010119935.1	s__Paenibacillus_Z lycopersici	77.7004	435	1812	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_009909185.1	s__Paenibacillus_Z glycinis	77.5037	475	1812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:54,372] [INFO] GTDB search result was written to GCF_004001085.1_ASM400108v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:54,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:54,376] [INFO] DFAST_QC result json was written to GCF_004001085.1_ASM400108v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:54,376] [INFO] DFAST_QC completed!
[2024-01-24 13:41:54,377] [INFO] Total running time: 0h1m26s