[2024-01-25 17:35:35,594] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,597] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference
[2024-01-25 17:35:36,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,717] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bfc194e-6428-47db-9c05-e21a787905ca/GCF_017874035.1_ASM1787403v1_genomic.fna.gz | prodigal -d GCF_017874035.1_ASM1787403v1_genomic.fna/cds.fna -a GCF_017874035.1_ASM1787403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:54,809] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:54,809] [INFO] Task started: HMMsearch
[2024-01-25 17:35:54,809] [INFO] Running command: hmmsearch --tblout GCF_017874035.1_ASM1787403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference/reference_markers.hmm GCF_017874035.1_ASM1787403v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:55,169] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:55,170] [INFO] Found 6/6 markers.
[2024-01-25 17:35:55,229] [INFO] Query marker FASTA was written to GCF_017874035.1_ASM1787403v1_genomic.fna/markers.fasta
[2024-01-25 17:35:55,230] [INFO] Task started: Blastn
[2024-01-25 17:35:55,230] [INFO] Running command: blastn -query GCF_017874035.1_ASM1787403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference/reference_markers.fasta -out GCF_017874035.1_ASM1787403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:55,835] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:55,838] [INFO] Selected 6 target genomes.
[2024-01-25 17:35:55,838] [INFO] Target genome list was writen to GCF_017874035.1_ASM1787403v1_genomic.fna/target_genomes.txt
[2024-01-25 17:35:55,856] [INFO] Task started: fastANI
[2024-01-25 17:35:55,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bfc194e-6428-47db-9c05-e21a787905ca/GCF_017874035.1_ASM1787403v1_genomic.fna.gz --refList GCF_017874035.1_ASM1787403v1_genomic.fna/target_genomes.txt --output GCF_017874035.1_ASM1787403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:07,223] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:07,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:07,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:07,230] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:07,230] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:07,230] [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 aceris	strain=DSM 24950	GCA_017874035.1	869555	869555	type	True	100.0	2627	2633	95	conclusive
Paenibacillus planticolens	strain=LMG 31457	GCA_013141725.1	2654976	2654976	type	True	87.628	1663	2633	95	below_threshold
Paenibacillus anseongense	strain=MAH-34	GCA_009757995.1	2682845	2682845	type	True	84.8729	1660	2633	95	below_threshold
Paenibacillus chondroitinus	strain=NBRC 15376	GCA_004000765.1	59842	59842	type	True	84.7406	1607	2633	95	below_threshold
Paenibacillus silvestris	strain=5J-6	GCA_009882985.1	2606219	2606219	type	True	84.5796	1637	2633	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.3874	94	2633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:07,231] [INFO] DFAST Taxonomy check result was written to GCF_017874035.1_ASM1787403v1_genomic.fna/tc_result.tsv
[2024-01-25 17:36:07,232] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:07,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:07,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference/checkm_data
[2024-01-25 17:36:07,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:07,304] [INFO] Task started: CheckM
[2024-01-25 17:36:07,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874035.1_ASM1787403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874035.1_ASM1787403v1_genomic.fna/checkm_input GCF_017874035.1_ASM1787403v1_genomic.fna/checkm_result
[2024-01-25 17:36:59,237] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:59,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:59,261] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:59,261] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:59,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874035.1_ASM1787403v1_genomic.fna/markers.fasta)
[2024-01-25 17:36:59,262] [INFO] Task started: Blastn
[2024-01-25 17:36:59,262] [INFO] Running command: blastn -query GCF_017874035.1_ASM1787403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5160d6e-467f-4273-a5d4-c453b6521e25/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874035.1_ASM1787403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:00,087] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:00,090] [INFO] Selected 5 target genomes.
[2024-01-25 17:37:00,091] [INFO] Target genome list was writen to GCF_017874035.1_ASM1787403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:00,094] [INFO] Task started: fastANI
[2024-01-25 17:37:00,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bfc194e-6428-47db-9c05-e21a787905ca/GCF_017874035.1_ASM1787403v1_genomic.fna.gz --refList GCF_017874035.1_ASM1787403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874035.1_ASM1787403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:10,675] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:10,680] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:10,680] [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_017874035.1	s__Paenibacillus_E aceris	100.0	2627	2633	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	conclusive
GCF_013141725.1	s__Paenibacillus_E planticolens	87.6217	1664	2633	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_004000765.1	s__Paenibacillus_E chondroitinus	84.7533	1605	2633	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	96.01	96.01	0.90	0.90	3	-
GCF_009882985.1	s__Paenibacillus_E silvestris	84.5747	1638	2633	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	84.3272	1596	2633	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 17:37:10,682] [INFO] GTDB search result was written to GCF_017874035.1_ASM1787403v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:10,682] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:10,690] [INFO] DFAST_QC result json was written to GCF_017874035.1_ASM1787403v1_genomic.fna/dqc_result.json
[2024-01-25 17:37:10,690] [INFO] DFAST_QC completed!
[2024-01-25 17:37:10,690] [INFO] Total running time: 0h1m35s