[2024-01-24 11:42:20,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference
[2024-01-24 11:42:24,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,523] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb7f5f5d-f147-48ac-9bb7-5184c0526766/GCF_014642075.1_ASM1464207v1_genomic.fna.gz | prodigal -d GCF_014642075.1_ASM1464207v1_genomic.fna/cds.fna -a GCF_014642075.1_ASM1464207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:42:56,252] [INFO] Task succeeded: Prodigal
[2024-01-24 11:42:56,252] [INFO] Task started: HMMsearch
[2024-01-24 11:42:56,253] [INFO] Running command: hmmsearch --tblout GCF_014642075.1_ASM1464207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference/reference_markers.hmm GCF_014642075.1_ASM1464207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:42:56,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:42:56,593] [INFO] Found 6/6 markers.
[2024-01-24 11:42:56,642] [INFO] Query marker FASTA was written to GCF_014642075.1_ASM1464207v1_genomic.fna/markers.fasta
[2024-01-24 11:42:56,642] [INFO] Task started: Blastn
[2024-01-24 11:42:56,642] [INFO] Running command: blastn -query GCF_014642075.1_ASM1464207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference/reference_markers.fasta -out GCF_014642075.1_ASM1464207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:42:57,231] [INFO] Task succeeded: Blastn
[2024-01-24 11:42:57,236] [INFO] Selected 20 target genomes.
[2024-01-24 11:42:57,236] [INFO] Target genome list was writen to GCF_014642075.1_ASM1464207v1_genomic.fna/target_genomes.txt
[2024-01-24 11:42:57,247] [INFO] Task started: fastANI
[2024-01-24 11:42:57,247] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7f5f5d-f147-48ac-9bb7-5184c0526766/GCF_014642075.1_ASM1464207v1_genomic.fna.gz --refList GCF_014642075.1_ASM1464207v1_genomic.fna/target_genomes.txt --output GCF_014642075.1_ASM1464207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:13,734] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:13,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:13,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:13,745] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:13,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:13,745] [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
Parapedobacter defluvii	strain=CGMCC 1.15342	GCA_014642075.1	2045106	2045106	type	True	100.0	1896	1899	95	conclusive
Parapedobacter indicus	strain=RK1	GCA_900113765.1	1477437	1477437	type	True	80.9417	931	1899	95	below_threshold
Parapedobacter indicus	strain=RK1	GCA_002934635.1	1477437	1477437	type	True	80.9059	931	1899	95	below_threshold
Sphingobacterium corticibacter	strain=2c-3	GCA_003076635.1	2171749	2171749	type	True	79.3627	55	1899	95	below_threshold
Parapedobacter pyrenivorans	strain=CGMCC 1.12195	GCA_014636865.1	1305674	1305674	type	True	78.7032	465	1899	95	below_threshold
Parapedobacter composti	strain=DSM 22900	GCA_900112315.1	623281	623281	type	True	78.5869	254	1899	95	below_threshold
Parapedobacter koreensis	strain=Jip14	GCA_900109365.1	332977	332977	type	True	78.5203	389	1899	95	below_threshold
Parapedobacter luteus	strain=DSM 22899	GCA_900168055.1	623280	623280	type	True	78.0486	296	1899	95	below_threshold
Parapedobacter lycopersici	strain=KACC 18788	GCA_024643285.1	1864939	1864939	type	True	77.75	180	1899	95	below_threshold
Parapedobacter soli	strain=KCTC 12984	GCA_025460835.1	416955	416955	type	True	77.5571	271	1899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:13,747] [INFO] DFAST Taxonomy check result was written to GCF_014642075.1_ASM1464207v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:13,747] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:13,748] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:13,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference/checkm_data
[2024-01-24 11:43:13,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:13,801] [INFO] Task started: CheckM
[2024-01-24 11:43:13,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642075.1_ASM1464207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642075.1_ASM1464207v1_genomic.fna/checkm_input GCF_014642075.1_ASM1464207v1_genomic.fna/checkm_result
[2024-01-24 11:44:38,735] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:38,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:38,757] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:38,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:38,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642075.1_ASM1464207v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:38,758] [INFO] Task started: Blastn
[2024-01-24 11:44:38,758] [INFO] Running command: blastn -query GCF_014642075.1_ASM1464207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d79e9fe-2700-4740-8c43-c12c580e42cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642075.1_ASM1464207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,577] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,581] [INFO] Selected 24 target genomes.
[2024-01-24 11:44:39,582] [INFO] Target genome list was writen to GCF_014642075.1_ASM1464207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:39,598] [INFO] Task started: fastANI
[2024-01-24 11:44:39,599] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7f5f5d-f147-48ac-9bb7-5184c0526766/GCF_014642075.1_ASM1464207v1_genomic.fna.gz --refList GCF_014642075.1_ASM1464207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642075.1_ASM1464207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:00,245] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:00,263] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:00,263] [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_014642075.1	s__Parapedobacter defluvii	100.0	1896	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113765.1	s__Parapedobacter indicus	80.9253	933	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014334135.1	s__Pseudosphingobacterium sp014334135	79.3727	77	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011030405.1	s__Sphingobacterium sp011030405	78.8835	70	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636865.1	s__Parapedobacter pyrenivorans	78.692	469	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112315.1	s__Parapedobacter composti	78.5764	254	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109365.1	s__Parapedobacter koreensis	78.5089	392	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168055.1	s__Parapedobacter luteus	78.044	297	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	99.02	99.02	0.90	0.90	2	-
GCF_008180195.1	s__Sphingobacterium phlebotomi	77.5308	55	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900109895.1	s__A37T11 sp900109895	76.159	70	1899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__A37T11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:00,265] [INFO] GTDB search result was written to GCF_014642075.1_ASM1464207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:00,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:00,270] [INFO] DFAST_QC result json was written to GCF_014642075.1_ASM1464207v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:00,270] [INFO] DFAST_QC completed!
[2024-01-24 11:45:00,270] [INFO] Total running time: 0h2m40s