[2024-01-24 14:39:44,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:44,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:44,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference
[2024-01-24 14:39:46,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:46,086] [INFO] Task started: Prodigal
[2024-01-24 14:39:46,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg51c287cd-63d4-4bcc-9d98-dc6d6dcae379/GCF_014640555.1_ASM1464055v1_genomic.fna.gz | prodigal -d GCF_014640555.1_ASM1464055v1_genomic.fna/cds.fna -a GCF_014640555.1_ASM1464055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:07,741] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:07,742] [INFO] Task started: HMMsearch
[2024-01-24 14:40:07,742] [INFO] Running command: hmmsearch --tblout GCF_014640555.1_ASM1464055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference/reference_markers.hmm GCF_014640555.1_ASM1464055v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:08,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:08,166] [INFO] Found 6/6 markers.
[2024-01-24 14:40:08,229] [INFO] Query marker FASTA was written to GCF_014640555.1_ASM1464055v1_genomic.fna/markers.fasta
[2024-01-24 14:40:08,230] [INFO] Task started: Blastn
[2024-01-24 14:40:08,230] [INFO] Running command: blastn -query GCF_014640555.1_ASM1464055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference/reference_markers.fasta -out GCF_014640555.1_ASM1464055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:08,853] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:08,860] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:08,861] [INFO] Target genome list was writen to GCF_014640555.1_ASM1464055v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:08,866] [INFO] Task started: fastANI
[2024-01-24 14:40:08,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c287cd-63d4-4bcc-9d98-dc6d6dcae379/GCF_014640555.1_ASM1464055v1_genomic.fna.gz --refList GCF_014640555.1_ASM1464055v1_genomic.fna/target_genomes.txt --output GCF_014640555.1_ASM1464055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:29,496] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:29,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:29,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:29,508] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:29,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:29,508] [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 marchantiophytorum	strain=CGMCC 1.15043	GCA_014640555.1	1619310	1619310	type	True	100.0	2668	2680	95	conclusive
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	84.8368	1584	2680	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	81.8	1094	2680	95	below_threshold
Paenibacillus frigoriresistens	strain=LMG 31322	GCA_013266765.1	1143711	1143711	type	True	81.7806	979	2680	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	81.7003	1091	2680	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	81.5693	1024	2680	95	below_threshold
Paenibacillus alginolyticus	strain=NBRC 15375	GCA_004000725.1	59839	59839	type	True	81.5552	998	2680	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	81.0786	947	2680	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	80.8962	981	2680	95	below_threshold
Paenibacillus pectinilyticus	strain=KCTC13222	GCA_001700435.1	512399	512399	type	True	80.4053	851	2680	95	below_threshold
Paenibacillus endophyticus	strain=CECT 8234	GCA_014192395.1	1294268	1294268	type	True	77.6744	118	2680	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.5902	70	2680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:29,511] [INFO] DFAST Taxonomy check result was written to GCF_014640555.1_ASM1464055v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:29,515] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:29,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:29,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference/checkm_data
[2024-01-24 14:40:29,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:29,599] [INFO] Task started: CheckM
[2024-01-24 14:40:29,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640555.1_ASM1464055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640555.1_ASM1464055v1_genomic.fna/checkm_input GCF_014640555.1_ASM1464055v1_genomic.fna/checkm_result
[2024-01-24 14:41:34,388] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:34,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:34,418] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:34,419] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:34,419] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640555.1_ASM1464055v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:34,420] [INFO] Task started: Blastn
[2024-01-24 14:41:34,420] [INFO] Running command: blastn -query GCF_014640555.1_ASM1464055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg314cc321-d910-4a55-b938-a04d6cd9170f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640555.1_ASM1464055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:35,233] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:35,236] [INFO] Selected 12 target genomes.
[2024-01-24 14:41:35,236] [INFO] Target genome list was writen to GCF_014640555.1_ASM1464055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:35,250] [INFO] Task started: fastANI
[2024-01-24 14:41:35,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c287cd-63d4-4bcc-9d98-dc6d6dcae379/GCF_014640555.1_ASM1464055v1_genomic.fna.gz --refList GCF_014640555.1_ASM1464055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640555.1_ASM1464055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:56,984] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:57,000] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:57,001] [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_014640555.1	s__Paenibacillus_E marchantiophytorum	100.0	2668	2680	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_002027705.1	s__Paenibacillus_E ferrarius	84.8139	1588	2680	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_013204855.1	s__Paenibacillus_E alba	84.5911	1590	2680	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_900103825.1	s__Paenibacillus_E sp900103825	81.8646	863	2680	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_013141715.1	s__Paenibacillus_E phytorum	81.7848	1098	2680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	95.60	95.60	0.80	0.80	2	-
GCF_000799595.1	s__Paenibacillus_E chondroitinus_A	81.6486	1005	2680	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_001426375.1	s__Paenibacillus_E sp001426375	81.6396	1050	2680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	98.92	98.92	0.95	0.95	2	-
GCF_001429545.1	s__Paenibacillus_E sp001429545	81.5877	946	2680	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_017874035.1	s__Paenibacillus_E aceris	81.2518	946	2680	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009882985.1	s__Paenibacillus_E silvestris	81.0884	946	2680	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_007829615.1	s__Paenibacillus_E sp007829615	80.8855	931	2680	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	80.4143	765	2680	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	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:57,002] [INFO] GTDB search result was written to GCF_014640555.1_ASM1464055v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:57,003] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:57,007] [INFO] DFAST_QC result json was written to GCF_014640555.1_ASM1464055v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:57,007] [INFO] DFAST_QC completed!
[2024-01-24 14:41:57,007] [INFO] Total running time: 0h2m12s