[2024-01-24 13:47:11,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference
[2024-01-24 13:47:12,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:12,627] [INFO] Task started: Prodigal
[2024-01-24 13:47:12,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg760ec254-4afb-4af2-b1ad-0d50c82a5aff/GCF_031454175.1_ASM3145417v1_genomic.fna.gz | prodigal -d GCF_031454175.1_ASM3145417v1_genomic.fna/cds.fna -a GCF_031454175.1_ASM3145417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:26,891] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:26,892] [INFO] Task started: HMMsearch
[2024-01-24 13:47:26,892] [INFO] Running command: hmmsearch --tblout GCF_031454175.1_ASM3145417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference/reference_markers.hmm GCF_031454175.1_ASM3145417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:27,214] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:27,216] [INFO] Found 6/6 markers.
[2024-01-24 13:47:27,260] [INFO] Query marker FASTA was written to GCF_031454175.1_ASM3145417v1_genomic.fna/markers.fasta
[2024-01-24 13:47:27,261] [INFO] Task started: Blastn
[2024-01-24 13:47:27,261] [INFO] Running command: blastn -query GCF_031454175.1_ASM3145417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference/reference_markers.fasta -out GCF_031454175.1_ASM3145417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,871] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,875] [INFO] Selected 17 target genomes.
[2024-01-24 13:47:27,875] [INFO] Target genome list was writen to GCF_031454175.1_ASM3145417v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:27,882] [INFO] Task started: fastANI
[2024-01-24 13:47:27,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg760ec254-4afb-4af2-b1ad-0d50c82a5aff/GCF_031454175.1_ASM3145417v1_genomic.fna.gz --refList GCF_031454175.1_ASM3145417v1_genomic.fna/target_genomes.txt --output GCF_031454175.1_ASM3145417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:43,707] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:43,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:43,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:43,726] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:43,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:43,726] [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 hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	99.9986	1840	1850	95	conclusive
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	79.2397	670	1850	95	below_threshold
Paenibacillus dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	79.149	650	1850	95	below_threshold
Paenibacillus wulumuqiensis	strain=Y24	GCA_000971965.1	1567107	1567107	type	True	79.0934	680	1850	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	77.6444	326	1850	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.432	156	1850	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.4197	78	1850	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	77.1795	141	1850	95	below_threshold
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	77.1322	107	1850	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	77.104	70	1850	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.9008	69	1850	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	76.6686	111	1850	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.6032	104	1850	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:43,728] [INFO] DFAST Taxonomy check result was written to GCF_031454175.1_ASM3145417v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:43,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:43,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:43,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference/checkm_data
[2024-01-24 13:47:43,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:43,783] [INFO] Task started: CheckM
[2024-01-24 13:47:43,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031454175.1_ASM3145417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031454175.1_ASM3145417v1_genomic.fna/checkm_input GCF_031454175.1_ASM3145417v1_genomic.fna/checkm_result
[2024-01-24 13:48:28,165] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:28,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:28,189] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:28,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:28,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031454175.1_ASM3145417v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:28,191] [INFO] Task started: Blastn
[2024-01-24 13:48:28,191] [INFO] Running command: blastn -query GCF_031454175.1_ASM3145417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18ccaa54-3784-4204-b5d1-a4fdf34ef75e/dqc_reference/reference_markers_gtdb.fasta -out GCF_031454175.1_ASM3145417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:28,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:28,958] [INFO] Selected 13 target genomes.
[2024-01-24 13:48:28,959] [INFO] Target genome list was writen to GCF_031454175.1_ASM3145417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:28,969] [INFO] Task started: fastANI
[2024-01-24 13:48:28,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg760ec254-4afb-4af2-b1ad-0d50c82a5aff/GCF_031454175.1_ASM3145417v1_genomic.fna.gz --refList GCF_031454175.1_ASM3145417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031454175.1_ASM3145417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:42,344] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:42,358] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:42,358] [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_014645615.1	s__Paenibacillus_J hunanensis	99.9986	1840	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001421015.2	s__Paenibacillus_J bovis	79.2497	668	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971985.1	s__Paenibacillus_J dauci	79.1565	647	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	97.87	97.87	0.93	0.93	2	-
GCF_000971965.1	s__Paenibacillus_J wulumuqiensis	79.1064	679	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721045.1	s__Paenibacillus_J nuruki	77.6444	326	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	98.40	98.40	0.93	0.93	2	-
GCF_016908805.1	s__Paenibacillus_J nicotianae	77.5706	359	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639235.1	s__Paenibacillus silvae	77.3838	154	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_004916975.1	s__Paenibacillus dokdonensis	77.1321	106	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761355.1	s__Paenibacillus_C lupini	77.1071	69	1850	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_013359935.1	s__Paenibacillus xylanilyticus	77.0001	146	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333315.1	s__Paenibacillus azoreducens	76.9954	96	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_003854965.1	s__Paenibacillus sp003854965	76.9223	71	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_013185195.1	s__Saccharibacillus qingshengii	76.6665	110	1850	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:42,360] [INFO] GTDB search result was written to GCF_031454175.1_ASM3145417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:42,361] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:42,364] [INFO] DFAST_QC result json was written to GCF_031454175.1_ASM3145417v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:42,364] [INFO] DFAST_QC completed!
[2024-01-24 13:48:42,364] [INFO] Total running time: 0h1m31s