[2024-01-24 13:40:28,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference
[2024-01-24 13:40:29,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,927] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgb32f16c1-9239-448a-a475-6194c4ee1f9a/GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/cds.fna -a GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,882] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,882] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,882] [INFO] Running command: hmmsearch --tblout GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference/reference_markers.hmm GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:50,225] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:50,226] [INFO] Found 6/6 markers.
[2024-01-24 13:40:50,290] [INFO] Query marker FASTA was written to GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:50,291] [INFO] Task started: Blastn
[2024-01-24 13:40:50,291] [INFO] Running command: blastn -query GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference/reference_markers.fasta -out GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,946] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,950] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:50,950] [INFO] Target genome list was writen to GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,957] [INFO] Task started: fastANI
[2024-01-24 13:40:50,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgb32f16c1-9239-448a-a475-6194c4ee1f9a/GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna.gz --refList GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:18,582] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:18,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:18,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:18,597] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:18,597] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:18,598] [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 jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	100.0	2322	2324	95	conclusive
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	99.9756	2288	2324	95	conclusive
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	93.5455	2068	2324	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	93.4083	1975	2324	95	below_threshold
Paenibacillus graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	93.3198	2040	2324	95	below_threshold
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	93.3115	1624	2324	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	93.1529	1677	2324	95	below_threshold
Paenibacillus riograndensis		GCA_000981585.1	483937	483937	type	True	93.114	2048	2324	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	92.8936	1422	2324	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	81.0526	1030	2324	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	80.0955	998	2324	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	79.3534	660	2324	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.2026	655	2324	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.4094	496	2324	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	77.595	228	2324	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.3252	262	2324	95	below_threshold
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	76.4643	136	2324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:18,599] [INFO] DFAST Taxonomy check result was written to GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:18,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:18,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:18,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference/checkm_data
[2024-01-24 13:41:18,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:18,670] [INFO] Task started: CheckM
[2024-01-24 13:41:18,671] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/checkm_input GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:42:15,472] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,496] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,497] [INFO] Task started: Blastn
[2024-01-24 13:42:15,497] [INFO] Running command: blastn -query GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fd401d7-c1cb-44af-88f9-c56669144ec9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,316] [INFO] Selected 8 target genomes.
[2024-01-24 13:42:16,316] [INFO] Target genome list was writen to GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,333] [INFO] Task started: fastANI
[2024-01-24 13:42:16,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgb32f16c1-9239-448a-a475-6194c4ee1f9a/GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna.gz --refList GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:30,428] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:30,434] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:30,435] [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_900102965.1	s__Paenibacillus jilunlii	100.0	2322	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	conclusive
GCF_016772475.1	s__Paenibacillus sonchi	93.5361	2069	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	99.97	99.97	1.00	1.00	2	-
GCF_000758705.1	s__Paenibacillus graminis	93.3198	2040	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000981585.1	s__Paenibacillus riograndensis	93.1291	2046	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	97.36	97.36	0.91	0.91	2	-
GCF_001909055.1	s__Paenibacillus helianthi	85.1155	1584	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.61	95.31	0.90	0.83	4	-
GCF_000374185.1	s__Paenibacillus sp000374185	83.2212	1386	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758725.1	s__Paenibacillus odorifer	79.3534	660	2324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:30,436] [INFO] GTDB search result was written to GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:30,437] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:30,440] [INFO] DFAST_QC result json was written to GCF_900102965.1_IMG-taxon_2667527409_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:30,440] [INFO] DFAST_QC completed!
[2024-01-24 13:42:30,440] [INFO] Total running time: 0h2m2s