[2024-01-24 14:28:07,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:07,852] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:07,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference
[2024-01-24 14:28:10,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,420] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg540498cb-f8c3-400c-a681-966f6b2f5538/GCF_028746185.1_ASM2874618v1_genomic.fna.gz | prodigal -d GCF_028746185.1_ASM2874618v1_genomic.fna/cds.fna -a GCF_028746185.1_ASM2874618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:33,657] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:33,658] [INFO] Task started: HMMsearch
[2024-01-24 14:28:33,658] [INFO] Running command: hmmsearch --tblout GCF_028746185.1_ASM2874618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference/reference_markers.hmm GCF_028746185.1_ASM2874618v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:34,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:34,096] [INFO] Found 6/6 markers.
[2024-01-24 14:28:34,165] [INFO] Query marker FASTA was written to GCF_028746185.1_ASM2874618v1_genomic.fna/markers.fasta
[2024-01-24 14:28:34,165] [INFO] Task started: Blastn
[2024-01-24 14:28:34,165] [INFO] Running command: blastn -query GCF_028746185.1_ASM2874618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference/reference_markers.fasta -out GCF_028746185.1_ASM2874618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:34,817] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:34,822] [INFO] Selected 16 target genomes.
[2024-01-24 14:28:34,822] [INFO] Target genome list was writen to GCF_028746185.1_ASM2874618v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:34,832] [INFO] Task started: fastANI
[2024-01-24 14:28:34,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg540498cb-f8c3-400c-a681-966f6b2f5538/GCF_028746185.1_ASM2874618v1_genomic.fna.gz --refList GCF_028746185.1_ASM2874618v1_genomic.fna/target_genomes.txt --output GCF_028746185.1_ASM2874618v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:00,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:00,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:00,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:00,776] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:29:00,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:29:00,776] [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 plantarum	strain=LMG 31461	GCA_013141695.1	2654975	2654975	type	True	90.1605	2118	2960	95	below_threshold
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	87.6564	2034	2960	95	below_threshold
Paenibacillus pectinilyticus	strain=KCTC13222	GCA_001700435.1	512399	512399	type	True	82.9289	1370	2960	95	below_threshold
Paenibacillus phytorum	strain=LMG 31458	GCA_013141715.1	2654977	2654977	type	True	80.7072	871	2960	95	below_threshold
Paenibacillus germinis	strain=LMG 31460	GCA_013141785.1	2654979	2654979	type	True	80.6317	905	2960	95	below_threshold
Paenibacillus alginolyticus	strain=DSM 5050	GCA_000422905.1	59839	59839	type	True	80.6018	855	2960	95	below_threshold
Paenibacillus ferrarius	strain=CY1	GCA_002027705.1	1469647	1469647	type	True	80.438	849	2960	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	80.046	815	2960	95	below_threshold
Paenibacillus aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	79.8911	787	2960	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	79.8873	795	2960	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	79.7619	847	2960	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	76.8393	56	2960	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.8249	113	2960	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	76.4101	51	2960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:00,778] [INFO] DFAST Taxonomy check result was written to GCF_028746185.1_ASM2874618v1_genomic.fna/tc_result.tsv
[2024-01-24 14:29:00,778] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:00,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:00,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference/checkm_data
[2024-01-24 14:29:00,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:00,871] [INFO] Task started: CheckM
[2024-01-24 14:29:00,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028746185.1_ASM2874618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028746185.1_ASM2874618v1_genomic.fna/checkm_input GCF_028746185.1_ASM2874618v1_genomic.fna/checkm_result
[2024-01-24 14:30:10,066] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:10,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:10,100] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:10,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:10,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028746185.1_ASM2874618v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:10,101] [INFO] Task started: Blastn
[2024-01-24 14:30:10,102] [INFO] Running command: blastn -query GCF_028746185.1_ASM2874618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb347496-7f91-41e6-bd0e-8a2116ec8674/dqc_reference/reference_markers_gtdb.fasta -out GCF_028746185.1_ASM2874618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:10,928] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:10,931] [INFO] Selected 6 target genomes.
[2024-01-24 14:30:10,932] [INFO] Target genome list was writen to GCF_028746185.1_ASM2874618v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:10,938] [INFO] Task started: fastANI
[2024-01-24 14:30:10,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg540498cb-f8c3-400c-a681-966f6b2f5538/GCF_028746185.1_ASM2874618v1_genomic.fna.gz --refList GCF_028746185.1_ASM2874618v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028746185.1_ASM2874618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:23,760] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:23,770] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:30:23,771] [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_013204845.1	s__Paenibacillus_E qinlingensis	99.9891	2923	2960	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_001428045.1	s__Paenibacillus_E sp001428045	90.6806	2064	2960	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_013141695.1	s__Paenibacillus_E plantarum	90.1679	2117	2960	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	88.5789	1812	2960	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	87.6616	2033	2960	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_001700435.1	s__Paenibacillus_E pectinilyticus	82.9519	1366	2960	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 14:30:23,773] [INFO] GTDB search result was written to GCF_028746185.1_ASM2874618v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:23,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:23,781] [INFO] DFAST_QC result json was written to GCF_028746185.1_ASM2874618v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:23,781] [INFO] DFAST_QC completed!
[2024-01-24 14:30:23,781] [INFO] Total running time: 0h2m16s