[2024-01-24 13:32:35,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:35,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:35,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference
[2024-01-24 13:32:36,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,466] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg80aa3ddc-9227-4709-9199-2001bd2d9880/GCF_002161855.1_ASM216185v1_genomic.fna.gz | prodigal -d GCF_002161855.1_ASM216185v1_genomic.fna/cds.fna -a GCF_002161855.1_ASM216185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:56,210] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:56,211] [INFO] Task started: HMMsearch
[2024-01-24 13:32:56,211] [INFO] Running command: hmmsearch --tblout GCF_002161855.1_ASM216185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference/reference_markers.hmm GCF_002161855.1_ASM216185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:56,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:56,703] [INFO] Found 6/6 markers.
[2024-01-24 13:32:56,757] [INFO] Query marker FASTA was written to GCF_002161855.1_ASM216185v1_genomic.fna/markers.fasta
[2024-01-24 13:32:56,757] [INFO] Task started: Blastn
[2024-01-24 13:32:56,757] [INFO] Running command: blastn -query GCF_002161855.1_ASM216185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference/reference_markers.fasta -out GCF_002161855.1_ASM216185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:57,404] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:57,408] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:57,408] [INFO] Target genome list was writen to GCF_002161855.1_ASM216185v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:57,432] [INFO] Task started: fastANI
[2024-01-24 13:32:57,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg80aa3ddc-9227-4709-9199-2001bd2d9880/GCF_002161855.1_ASM216185v1_genomic.fna.gz --refList GCF_002161855.1_ASM216185v1_genomic.fna/target_genomes.txt --output GCF_002161855.1_ASM216185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:14,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:14,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:14,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:14,157] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:14,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:14,158] [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 thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	100.0	2149	2152	95	conclusive
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	99.9975	2152	2152	95	conclusive
Paenibacillus thiaminolyticus	strain=NBRC 15656	GCA_004001005.1	49283	49283	type	True	99.9435	2026	2152	95	conclusive
Paenibacillus popilliae	strain=ATCC 14706	GCA_000315235.1	78057	78057	type	True	88.8109	864	2152	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.8615	152	2152	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.6643	109	2152	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	76.6573	140	2152	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	76.5653	183	2152	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.4372	194	2152	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.4259	98	2152	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	76.2151	133	2152	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	76.1734	97	2152	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.1097	121	2152	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.0463	145	2152	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	75.89	98	2152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:14,160] [INFO] DFAST Taxonomy check result was written to GCF_002161855.1_ASM216185v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:14,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:14,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:14,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference/checkm_data
[2024-01-24 13:33:14,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:14,228] [INFO] Task started: CheckM
[2024-01-24 13:33:14,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002161855.1_ASM216185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002161855.1_ASM216185v1_genomic.fna/checkm_input GCF_002161855.1_ASM216185v1_genomic.fna/checkm_result
[2024-01-24 13:34:10,940] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:10,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:10,965] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:10,965] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:10,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002161855.1_ASM216185v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:10,966] [INFO] Task started: Blastn
[2024-01-24 13:34:10,966] [INFO] Running command: blastn -query GCF_002161855.1_ASM216185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01e48673-01ca-4f0d-a674-2eb8a39e5c0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002161855.1_ASM216185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:11,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:11,786] [INFO] Selected 6 target genomes.
[2024-01-24 13:34:11,787] [INFO] Target genome list was writen to GCF_002161855.1_ASM216185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:11,804] [INFO] Task started: fastANI
[2024-01-24 13:34:11,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg80aa3ddc-9227-4709-9199-2001bd2d9880/GCF_002161855.1_ASM216185v1_genomic.fna.gz --refList GCF_002161855.1_ASM216185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002161855.1_ASM216185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:22,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:22,255] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:22,256] [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_007066085.1	s__Paenibacillus_B thiaminolyticus	99.9975	2152	2152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.67	95.07	0.96	0.85	7	conclusive
GCF_000245555.1	s__Paenibacillus_B dendritiformis_A	92.785	1732	2152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.57	96.94	0.92	0.90	3	-
GCF_018403065.1	s__Paenibacillus_B dendritiformis_B	91.2458	1614	2152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015845845.1	s__Paenibacillus_B dendritiformis_C	91.0321	1624	2152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266915.1	s__Paenibacillus_B sp900539405	90.6008	1676	2152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	99.54	99.32	0.96	0.95	4	-
GCF_000315235.1	s__Paenibacillus_B popilliae	88.7937	865	2152	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:22,258] [INFO] GTDB search result was written to GCF_002161855.1_ASM216185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:22,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:22,265] [INFO] DFAST_QC result json was written to GCF_002161855.1_ASM216185v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:22,265] [INFO] DFAST_QC completed!
[2024-01-24 13:34:22,265] [INFO] Total running time: 0h1m47s