[2024-01-25 20:18:21,047] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:21,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:21,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference
[2024-01-25 20:18:22,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,157] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,157] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e45052a-34bc-4e19-b9b0-d1414d413459/GCF_001700435.1_ASM170043v1_genomic.fna.gz | prodigal -d GCF_001700435.1_ASM170043v1_genomic.fna/cds.fna -a GCF_001700435.1_ASM170043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:39,673] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:39,674] [INFO] Task started: HMMsearch
[2024-01-25 20:18:39,674] [INFO] Running command: hmmsearch --tblout GCF_001700435.1_ASM170043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference/reference_markers.hmm GCF_001700435.1_ASM170043v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:39,988] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:39,989] [INFO] Found 6/6 markers.
[2024-01-25 20:18:40,046] [INFO] Query marker FASTA was written to GCF_001700435.1_ASM170043v1_genomic.fna/markers.fasta
[2024-01-25 20:18:40,046] [INFO] Task started: Blastn
[2024-01-25 20:18:40,046] [INFO] Running command: blastn -query GCF_001700435.1_ASM170043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference/reference_markers.fasta -out GCF_001700435.1_ASM170043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:40,594] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:40,597] [INFO] Selected 16 target genomes.
[2024-01-25 20:18:40,597] [INFO] Target genome list was writen to GCF_001700435.1_ASM170043v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:40,612] [INFO] Task started: fastANI
[2024-01-25 20:18:40,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e45052a-34bc-4e19-b9b0-d1414d413459/GCF_001700435.1_ASM170043v1_genomic.fna.gz --refList GCF_001700435.1_ASM170043v1_genomic.fna/target_genomes.txt --output GCF_001700435.1_ASM170043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:01,541] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:01,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:01,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:01,551] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:01,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:01,551] [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 pectinilyticus	strain=KCTC13222	GCA_001700435.1	512399	512399	type	True	100.0	2611	2613	95	conclusive
Paenibacillus plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	83.4461	1418	2613	95	below_threshold
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	82.3084	1244	2613	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	80.7347	796	2613	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	80.7308	794	2613	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	80.7252	819	2613	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	80.6939	842	2613	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	80.6091	891	2613	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	80.6056	824	2613	95	below_threshold
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	80.2612	727	2613	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	80.076	789	2613	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	76.6238	61	2613	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.2248	66	2613	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:01,553] [INFO] DFAST Taxonomy check result was written to GCF_001700435.1_ASM170043v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:01,553] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:01,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:01,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference/checkm_data
[2024-01-25 20:19:01,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:01,626] [INFO] Task started: CheckM
[2024-01-25 20:19:01,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001700435.1_ASM170043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001700435.1_ASM170043v1_genomic.fna/checkm_input GCF_001700435.1_ASM170043v1_genomic.fna/checkm_result
[2024-01-25 20:19:54,409] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:54,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:54,430] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:54,430] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:54,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001700435.1_ASM170043v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:54,431] [INFO] Task started: Blastn
[2024-01-25 20:19:54,431] [INFO] Running command: blastn -query GCF_001700435.1_ASM170043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d0c80ef-bac5-49ac-a7bd-35c964001d31/dqc_reference/reference_markers_gtdb.fasta -out GCF_001700435.1_ASM170043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:55,220] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:55,223] [INFO] Selected 8 target genomes.
[2024-01-25 20:19:55,223] [INFO] Target genome list was writen to GCF_001700435.1_ASM170043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:55,229] [INFO] Task started: fastANI
[2024-01-25 20:19:55,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e45052a-34bc-4e19-b9b0-d1414d413459/GCF_001700435.1_ASM170043v1_genomic.fna.gz --refList GCF_001700435.1_ASM170043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001700435.1_ASM170043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:08,274] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:08,279] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:08,280] [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_001700435.1	s__Paenibacillus_E pectinilyticus	100.0	2611	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013141695.1	s__Paenibacillus_E plantarum	83.4489	1417	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620565.1	s__Paenibacillus_E sp000620565	83.2712	1324	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428045.1	s__Paenibacillus_E sp001428045	83.1797	1358	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428105.1	s__Paenibacillus_E sp001428105	83.0456	1213	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204845.1	s__Paenibacillus_E qinlingensis	82.9142	1371	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653565.1	s__Paenibacillus_E oryzisoli	82.2935	1246	2613	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:08,281] [INFO] GTDB search result was written to GCF_001700435.1_ASM170043v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:08,281] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:08,284] [INFO] DFAST_QC result json was written to GCF_001700435.1_ASM170043v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:08,284] [INFO] DFAST_QC completed!
[2024-01-25 20:20:08,284] [INFO] Total running time: 0h1m47s