[2024-01-24 13:48:42,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:42,980] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:42,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference
[2024-01-24 13:48:44,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,280] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,280] [INFO] Running command: gunzip -c /var/lib/cwl/stgf466124d-0422-491d-94db-0771acbf8166/GCF_008635795.1_ASM863579v1_genomic.fna.gz | prodigal -d GCF_008635795.1_ASM863579v1_genomic.fna/cds.fna -a GCF_008635795.1_ASM863579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:03,035] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:03,036] [INFO] Task started: HMMsearch
[2024-01-24 13:49:03,036] [INFO] Running command: hmmsearch --tblout GCF_008635795.1_ASM863579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference/reference_markers.hmm GCF_008635795.1_ASM863579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:03,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:03,381] [INFO] Found 6/6 markers.
[2024-01-24 13:49:03,438] [INFO] Query marker FASTA was written to GCF_008635795.1_ASM863579v1_genomic.fna/markers.fasta
[2024-01-24 13:49:03,439] [INFO] Task started: Blastn
[2024-01-24 13:49:03,439] [INFO] Running command: blastn -query GCF_008635795.1_ASM863579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference/reference_markers.fasta -out GCF_008635795.1_ASM863579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:04,066] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:04,070] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:04,071] [INFO] Target genome list was writen to GCF_008635795.1_ASM863579v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:04,079] [INFO] Task started: fastANI
[2024-01-24 13:49:04,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgf466124d-0422-491d-94db-0771acbf8166/GCF_008635795.1_ASM863579v1_genomic.fna.gz --refList GCF_008635795.1_ASM863579v1_genomic.fna/target_genomes.txt --output GCF_008635795.1_ASM863579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:24,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:24,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:24,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:24,908] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:24,908] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:24,908] [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 tepidiphilus	strain=SYSU G01001	GCA_008635795.1	2608683	2608683	type	True	100.0	2226	2229	95	conclusive
Paenibacillus tengchongensis	strain=SYSU G01003	GCA_008973665.1	2608684	2608684	type	True	86.1897	1692	2229	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	80.04	988	2229	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.911	855	2229	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	79.7129	844	2229	95	below_threshold
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	79.6768	866	2229	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	79.6758	986	2229	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	79.6473	643	2229	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	79.5488	977	2229	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	79.5098	858	2229	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	79.3365	880	2229	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	79.3256	917	2229	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	78.7976	514	2229	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.3945	469	2229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:24,916] [INFO] DFAST Taxonomy check result was written to GCF_008635795.1_ASM863579v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:24,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:24,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:24,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference/checkm_data
[2024-01-24 13:49:24,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:24,983] [INFO] Task started: CheckM
[2024-01-24 13:49:24,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008635795.1_ASM863579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008635795.1_ASM863579v1_genomic.fna/checkm_input GCF_008635795.1_ASM863579v1_genomic.fna/checkm_result
[2024-01-24 13:50:21,399] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:21,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,423] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:21,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:21,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008635795.1_ASM863579v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:21,425] [INFO] Task started: Blastn
[2024-01-24 13:50:21,425] [INFO] Running command: blastn -query GCF_008635795.1_ASM863579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53ad2c38-5037-45d2-9f50-11a13387baa4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008635795.1_ASM863579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:22,316] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:22,321] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:22,321] [INFO] Target genome list was writen to GCF_008635795.1_ASM863579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:22,340] [INFO] Task started: fastANI
[2024-01-24 13:50:22,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgf466124d-0422-491d-94db-0771acbf8166/GCF_008635795.1_ASM863579v1_genomic.fna.gz --refList GCF_008635795.1_ASM863579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008635795.1_ASM863579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:49,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:49,221] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:49,221] [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_008635795.1	s__Paenibacillus tepidiphilus	100.0	2226	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008973665.1	s__Paenibacillus tengchongensis	86.1897	1692	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099765.1	s__Paenibacillus typhae	80.0363	989	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
GCF_001517085.1	s__Paenibacillus sp001517085	79.8307	992	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758525.1	s__Paenibacillus sp000758525	79.7911	921	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.46	97.46	0.89	0.89	2	-
GCF_000758625.1	s__Paenibacillus sp000758625	79.7621	1004	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016772475.1	s__Paenibacillus sonchi	79.7021	847	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	99.97	99.97	1.00	1.00	2	-
GCF_000758665.1	s__Paenibacillus borealis	79.6807	984	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981585.1	s__Paenibacillus riograndensis	79.6682	866	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	97.36	97.36	0.91	0.91	2	-
GCF_000723885.1	s__Paenibacillus camerounensis	79.6419	924	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.67	95.67	0.88	0.88	2	-
GCF_900102965.1	s__Paenibacillus jilunlii	79.5644	820	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_013141775.1	s__Paenibacillus phytohabitans	79.5333	980	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_013204885.1	s__Paenibacillus tritici	79.4987	859	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
GCF_017874735.1	s__Paenibacillus silagei	79.3391	877	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	79.3086	899	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001955925.1	s__Paenibacillus sp001955925	79.1729	845	2229	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:49,223] [INFO] GTDB search result was written to GCF_008635795.1_ASM863579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:49,224] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:49,231] [INFO] DFAST_QC result json was written to GCF_008635795.1_ASM863579v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:49,232] [INFO] DFAST_QC completed!
[2024-01-24 13:50:49,232] [INFO] Total running time: 0h2m6s