[2024-01-24 12:21:57,578] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference
[2024-01-24 12:21:59,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,005] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,005] [INFO] Running command: gunzip -c /var/lib/cwl/stgdceb77a7-101a-4bf9-aead-f745823b748d/GCF_000758705.1_ASM75870v1_genomic.fna.gz | prodigal -d GCF_000758705.1_ASM75870v1_genomic.fna/cds.fna -a GCF_000758705.1_ASM75870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:19,469] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:19,469] [INFO] Task started: HMMsearch
[2024-01-24 12:22:19,469] [INFO] Running command: hmmsearch --tblout GCF_000758705.1_ASM75870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference/reference_markers.hmm GCF_000758705.1_ASM75870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:19,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:19,825] [INFO] Found 6/6 markers.
[2024-01-24 12:22:20,317] [INFO] Query marker FASTA was written to GCF_000758705.1_ASM75870v1_genomic.fna/markers.fasta
[2024-01-24 12:22:20,317] [INFO] Task started: Blastn
[2024-01-24 12:22:20,318] [INFO] Running command: blastn -query GCF_000758705.1_ASM75870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference/reference_markers.fasta -out GCF_000758705.1_ASM75870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:20,951] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:20,955] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:20,956] [INFO] Target genome list was writen to GCF_000758705.1_ASM75870v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:20,966] [INFO] Task started: fastANI
[2024-01-24 12:22:20,966] [INFO] Running command: fastANI --query /var/lib/cwl/stgdceb77a7-101a-4bf9-aead-f745823b748d/GCF_000758705.1_ASM75870v1_genomic.fna.gz --refList GCF_000758705.1_ASM75870v1_genomic.fna/target_genomes.txt --output GCF_000758705.1_ASM75870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:42,760] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:42,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:42,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:42,772] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:42,772] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:22:42,773] [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 graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	100.0	2388	2388	95	inconclusive
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	99.7453	1930	2388	95	inconclusive
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	96.7101	2024	2388	95	inconclusive
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	93.3032	2049	2388	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	93.2792	2030	2388	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	92.4673	2008	2388	95	below_threshold
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	92.245	1558	2388	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	81.1151	1048	2388	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	79.9536	991	2388	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.3615	618	2388	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	78.1984	492	2388	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.1146	158	2388	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	76.5521	150	2388	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,775] [INFO] DFAST Taxonomy check result was written to GCF_000758705.1_ASM75870v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:42,776] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:42,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:42,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference/checkm_data
[2024-01-24 12:22:42,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:42,842] [INFO] Task started: CheckM
[2024-01-24 12:22:42,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000758705.1_ASM75870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000758705.1_ASM75870v1_genomic.fna/checkm_input GCF_000758705.1_ASM75870v1_genomic.fna/checkm_result
[2024-01-24 12:23:41,637] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:41,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:41,663] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:41,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:41,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000758705.1_ASM75870v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:41,663] [INFO] Task started: Blastn
[2024-01-24 12:23:41,663] [INFO] Running command: blastn -query GCF_000758705.1_ASM75870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg732975f3-4d89-46c4-8d85-fed3d9e33c86/dqc_reference/reference_markers_gtdb.fasta -out GCF_000758705.1_ASM75870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:42,536] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:42,539] [INFO] Selected 10 target genomes.
[2024-01-24 12:23:42,539] [INFO] Target genome list was writen to GCF_000758705.1_ASM75870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:42,548] [INFO] Task started: fastANI
[2024-01-24 12:23:42,548] [INFO] Running command: fastANI --query /var/lib/cwl/stgdceb77a7-101a-4bf9-aead-f745823b748d/GCF_000758705.1_ASM75870v1_genomic.fna.gz --refList GCF_000758705.1_ASM75870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000758705.1_ASM75870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:57,417] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:57,424] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:57,424] [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_000758705.1	s__Paenibacillus graminis	100.0	2388	2388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900102965.1	s__Paenibacillus jilunlii	93.3032	2049	2388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_016772475.1	s__Paenibacillus sonchi	92.4533	2011	2388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.4356	99.97	99.97	1.00	1.00	2	-
GCF_000981585.1	s__Paenibacillus riograndensis	92.1549	2015	2388	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	85.0934	1593	2388	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	83.1785	1380	2388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002192415.1	s__Paenibacillus donghaensis	80.0558	959	2388	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:57,426] [INFO] GTDB search result was written to GCF_000758705.1_ASM75870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:57,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:57,430] [INFO] DFAST_QC result json was written to GCF_000758705.1_ASM75870v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:57,430] [INFO] DFAST_QC completed!
[2024-01-24 12:23:57,430] [INFO] Total running time: 0h1m60s