[2024-01-24 11:34:54,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:54,279] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:54,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference
[2024-01-24 11:34:56,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,095] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg537ba8e6-8c05-4ee9-b526-f80dcdc380a0/GCF_018966525.1_ASM1896652v1_genomic.fna.gz | prodigal -d GCF_018966525.1_ASM1896652v1_genomic.fna/cds.fna -a GCF_018966525.1_ASM1896652v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:13,433] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:13,433] [INFO] Task started: HMMsearch
[2024-01-24 11:35:13,434] [INFO] Running command: hmmsearch --tblout GCF_018966525.1_ASM1896652v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference/reference_markers.hmm GCF_018966525.1_ASM1896652v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:13,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:13,774] [INFO] Found 6/6 markers.
[2024-01-24 11:35:13,826] [INFO] Query marker FASTA was written to GCF_018966525.1_ASM1896652v1_genomic.fna/markers.fasta
[2024-01-24 11:35:13,827] [INFO] Task started: Blastn
[2024-01-24 11:35:13,827] [INFO] Running command: blastn -query GCF_018966525.1_ASM1896652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference/reference_markers.fasta -out GCF_018966525.1_ASM1896652v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:14,430] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:14,434] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:14,435] [INFO] Target genome list was writen to GCF_018966525.1_ASM1896652v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:14,442] [INFO] Task started: fastANI
[2024-01-24 11:35:14,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg537ba8e6-8c05-4ee9-b526-f80dcdc380a0/GCF_018966525.1_ASM1896652v1_genomic.fna.gz --refList GCF_018966525.1_ASM1896652v1_genomic.fna/target_genomes.txt --output GCF_018966525.1_ASM1896652v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,684] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:31,702] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:31,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:31,702] [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 sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	100.0	1955	1955	95	conclusive
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	99.9877	1907	1955	95	conclusive
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	90.7593	1098	1955	95	below_threshold
Paenibacillus forsythiae	strain=T98	GCA_000520735.1	365616	365616	type	True	87.4681	1033	1955	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	86.7269	1336	1955	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	85.3308	1309	1955	95	below_threshold
Paenibacillus apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	85.2765	1312	1955	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	78.6101	512	1955	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	78.2682	162	1955	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	78.1887	396	1955	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	78.041	428	1955	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	77.9626	451	1955	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	76.8649	127	1955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,704] [INFO] DFAST Taxonomy check result was written to GCF_018966525.1_ASM1896652v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:31,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:31,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:31,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference/checkm_data
[2024-01-24 11:35:31,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:31,762] [INFO] Task started: CheckM
[2024-01-24 11:35:31,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018966525.1_ASM1896652v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018966525.1_ASM1896652v1_genomic.fna/checkm_input GCF_018966525.1_ASM1896652v1_genomic.fna/checkm_result
[2024-01-24 11:36:24,674] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:24,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:24,697] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:24,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:24,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018966525.1_ASM1896652v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:24,698] [INFO] Task started: Blastn
[2024-01-24 11:36:24,699] [INFO] Running command: blastn -query GCF_018966525.1_ASM1896652v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg753c784a-49ba-4420-8a07-a3e25d652379/dqc_reference/reference_markers_gtdb.fasta -out GCF_018966525.1_ASM1896652v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:25,529] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:25,532] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:25,533] [INFO] Target genome list was writen to GCF_018966525.1_ASM1896652v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:25,539] [INFO] Task started: fastANI
[2024-01-24 11:36:25,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg537ba8e6-8c05-4ee9-b526-f80dcdc380a0/GCF_018966525.1_ASM1896652v1_genomic.fna.gz --refList GCF_018966525.1_ASM1896652v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018966525.1_ASM1896652v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:36,468] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:36,480] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:36,480] [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_018966525.1	s__Paenibacillus sophorae	100.0	1955	1955	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_000756615.1	s__Paenibacillus durus	92.1416	1517	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000993825.1	s__Paenibacillus durus_B	91.266	1456	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000520715.1	s__Paenibacillus zanthoxyli	90.7482	1099	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520735.1	s__Paenibacillus forsythiae	87.482	1031	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854965.1	s__Paenibacillus sp003854965	86.7208	1337	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_009664975.1	s__Paenibacillus sp009664975	77.6721	384	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212125.1	s__Cohnella nanjingensis	76.8824	127	1955	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:36,482] [INFO] GTDB search result was written to GCF_018966525.1_ASM1896652v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:36,482] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:36,485] [INFO] DFAST_QC result json was written to GCF_018966525.1_ASM1896652v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:36,485] [INFO] DFAST_QC completed!
[2024-01-24 11:36:36,485] [INFO] Total running time: 0h1m42s