[2024-01-24 10:47:40,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stge52f95c2-67b6-4931-ad93-c42f9e3453f8/GCF_014645615.1_ASM1464561v1_genomic.fna.gz | prodigal -d GCF_014645615.1_ASM1464561v1_genomic.fna/cds.fna -a GCF_014645615.1_ASM1464561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:58,908] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:58,909] [INFO] Task started: HMMsearch
[2024-01-24 10:47:58,909] [INFO] Running command: hmmsearch --tblout GCF_014645615.1_ASM1464561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference/reference_markers.hmm GCF_014645615.1_ASM1464561v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:59,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:59,251] [INFO] Found 6/6 markers.
[2024-01-24 10:47:59,291] [INFO] Query marker FASTA was written to GCF_014645615.1_ASM1464561v1_genomic.fna/markers.fasta
[2024-01-24 10:47:59,292] [INFO] Task started: Blastn
[2024-01-24 10:47:59,292] [INFO] Running command: blastn -query GCF_014645615.1_ASM1464561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference/reference_markers.fasta -out GCF_014645615.1_ASM1464561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,874] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,878] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:59,879] [INFO] Target genome list was writen to GCF_014645615.1_ASM1464561v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:59,911] [INFO] Task started: fastANI
[2024-01-24 10:47:59,912] [INFO] Running command: fastANI --query /var/lib/cwl/stge52f95c2-67b6-4931-ad93-c42f9e3453f8/GCF_014645615.1_ASM1464561v1_genomic.fna.gz --refList GCF_014645615.1_ASM1464561v1_genomic.fna/target_genomes.txt --output GCF_014645615.1_ASM1464561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:16,191] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:16,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:16,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:16,202] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:16,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:16,203] [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	100.0	1864	1868	95	conclusive
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	79.2483	677	1868	95	below_threshold
Paenibacillus dauci	strain=H9	GCA_000971985.1	1567106	1567106	type	True	79.164	641	1868	95	below_threshold
Paenibacillus wulumuqiensis	strain=Y24	GCA_000971965.1	1567107	1567107	type	True	79.0923	675	1868	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.7211	157	1868	95	below_threshold
Paenibacillus nuruki	strain=TI45-13ar	GCA_001721045.1	1886670	1886670	type	True	77.6085	331	1868	95	below_threshold
Paenibacillus taichungensis	strain=DSM 19942	GCA_013359905.1	484184	484184	type	True	77.2181	136	1868	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.0737	83	1868	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.0249	66	1868	95	below_threshold
Paenibacillus dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	76.9453	113	1868	95	below_threshold
Paenibacillus lupini	strain=CECT 8235	GCA_011761355.1	1450204	1450204	type	True	76.9426	72	1868	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	76.5266	116	1868	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.3854	105	1868	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,204] [INFO] DFAST Taxonomy check result was written to GCF_014645615.1_ASM1464561v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:16,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:16,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:16,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference/checkm_data
[2024-01-24 10:48:16,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:16,259] [INFO] Task started: CheckM
[2024-01-24 10:48:16,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645615.1_ASM1464561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645615.1_ASM1464561v1_genomic.fna/checkm_input GCF_014645615.1_ASM1464561v1_genomic.fna/checkm_result
[2024-01-24 10:49:01,250] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:01,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:01,277] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:01,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:01,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645615.1_ASM1464561v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:01,278] [INFO] Task started: Blastn
[2024-01-24 10:49:01,278] [INFO] Running command: blastn -query GCF_014645615.1_ASM1464561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf91330a7-e731-42d3-be43-cc1f6d526305/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645615.1_ASM1464561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:02,085] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:02,090] [INFO] Selected 13 target genomes.
[2024-01-24 10:49:02,090] [INFO] Target genome list was writen to GCF_014645615.1_ASM1464561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:02,118] [INFO] Task started: fastANI
[2024-01-24 10:49:02,118] [INFO] Running command: fastANI --query /var/lib/cwl/stge52f95c2-67b6-4931-ad93-c42f9e3453f8/GCF_014645615.1_ASM1464561v1_genomic.fna.gz --refList GCF_014645615.1_ASM1464561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645615.1_ASM1464561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:16,043] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:16,057] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:16,058] [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	100.0	1864	1868	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	79.2411	678	1868	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	79.1695	642	1868	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	79.0947	673	1868	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	77.7222	157	1868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_001721045.1	s__Paenibacillus_J nuruki	77.6085	331	1868	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	77.5814	356	1868	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_003854965.1	s__Paenibacillus sp003854965	77.1281	66	1868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_004916975.1	s__Paenibacillus dokdonensis	76.9462	112	1868	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	76.9432	102	1868	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_013359935.1	s__Paenibacillus xylanilyticus	76.8914	148	1868	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	76.8214	70	1868	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_013185195.1	s__Saccharibacillus qingshengii	76.5266	116	1868	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 10:49:16,061] [INFO] GTDB search result was written to GCF_014645615.1_ASM1464561v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:16,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:16,066] [INFO] DFAST_QC result json was written to GCF_014645615.1_ASM1464561v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:16,066] [INFO] DFAST_QC completed!
[2024-01-24 10:49:16,066] [INFO] Total running time: 0h1m35s