[2024-01-24 12:30:05,380] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,382] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference
[2024-01-24 12:30:07,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,249] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cf9a674-3257-438b-bada-d1768130ec44/GCF_024643285.1_ASM2464328v1_genomic.fna.gz | prodigal -d GCF_024643285.1_ASM2464328v1_genomic.fna/cds.fna -a GCF_024643285.1_ASM2464328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:23,497] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:23,497] [INFO] Task started: HMMsearch
[2024-01-24 12:30:23,497] [INFO] Running command: hmmsearch --tblout GCF_024643285.1_ASM2464328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference/reference_markers.hmm GCF_024643285.1_ASM2464328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:23,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:23,763] [INFO] Found 6/6 markers.
[2024-01-24 12:30:23,791] [INFO] Query marker FASTA was written to GCF_024643285.1_ASM2464328v1_genomic.fna/markers.fasta
[2024-01-24 12:30:23,791] [INFO] Task started: Blastn
[2024-01-24 12:30:23,791] [INFO] Running command: blastn -query GCF_024643285.1_ASM2464328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference/reference_markers.fasta -out GCF_024643285.1_ASM2464328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:24,338] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:24,340] [INFO] Selected 15 target genomes.
[2024-01-24 12:30:24,341] [INFO] Target genome list was writen to GCF_024643285.1_ASM2464328v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:24,344] [INFO] Task started: fastANI
[2024-01-24 12:30:24,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cf9a674-3257-438b-bada-d1768130ec44/GCF_024643285.1_ASM2464328v1_genomic.fna.gz --refList GCF_024643285.1_ASM2464328v1_genomic.fna/target_genomes.txt --output GCF_024643285.1_ASM2464328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:37,282] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:37,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:37,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:37,289] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:37,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:37,289] [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 lycopersici	strain=KACC 18788	GCA_024643285.1	1864939	1864939	type	True	100.0	1197	1198	95	conclusive
Parapedobacter pyrenivorans	strain=CGMCC 1.12195	GCA_014636865.1	1305674	1305674	type	True	77.9204	187	1198	95	below_threshold
Parapedobacter indicus	strain=RK1	GCA_002934635.1	1477437	1477437	type	True	77.7944	157	1198	95	below_threshold
Parapedobacter indicus	strain=RK1	GCA_900113765.1	1477437	1477437	type	True	77.7733	158	1198	95	below_threshold
Parapedobacter defluvii	strain=CGMCC 1.15342	GCA_014642075.1	2045106	2045106	type	True	77.7607	180	1198	95	below_threshold
Parapedobacter composti	strain=DSM 22900	GCA_900112315.1	623281	623281	type	True	77.2771	157	1198	95	below_threshold
Parapedobacter luteus	strain=DSM 22899	GCA_900168055.1	623280	623280	type	True	77.246	163	1198	95	below_threshold
Parapedobacter koreensis	strain=Jip14	GCA_900109365.1	332977	332977	type	True	77.039	173	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,291] [INFO] DFAST Taxonomy check result was written to GCF_024643285.1_ASM2464328v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:37,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:37,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:37,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference/checkm_data
[2024-01-24 12:30:37,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:37,344] [INFO] Task started: CheckM
[2024-01-24 12:30:37,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024643285.1_ASM2464328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024643285.1_ASM2464328v1_genomic.fna/checkm_input GCF_024643285.1_ASM2464328v1_genomic.fna/checkm_result
[2024-01-24 12:31:23,649] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:23,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:23,661] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:23,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:23,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024643285.1_ASM2464328v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:23,662] [INFO] Task started: Blastn
[2024-01-24 12:31:23,662] [INFO] Running command: blastn -query GCF_024643285.1_ASM2464328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg247e08ae-3d52-44d9-86f5-a18c512bf475/dqc_reference/reference_markers_gtdb.fasta -out GCF_024643285.1_ASM2464328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:24,489] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:24,491] [INFO] Selected 27 target genomes.
[2024-01-24 12:31:24,491] [INFO] Target genome list was writen to GCF_024643285.1_ASM2464328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:24,504] [INFO] Task started: fastANI
[2024-01-24 12:31:24,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cf9a674-3257-438b-bada-d1768130ec44/GCF_024643285.1_ASM2464328v1_genomic.fna.gz --refList GCF_024643285.1_ASM2464328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024643285.1_ASM2464328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:46,643] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:46,648] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:31:46,648] [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_014636865.1	s__Parapedobacter pyrenivorans	77.8933	190	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113765.1	s__Parapedobacter indicus	77.7692	159	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014642075.1	s__Parapedobacter defluvii	77.7547	182	1198	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	77.2788	157	1198	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	77.2295	165	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	99.02	99.02	0.90	0.90	2	-
GCF_900109365.1	s__Parapedobacter koreensis	77.0403	175	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274585.1	s__BS3 sp008274585	76.2337	53	1198	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__BS3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:46,650] [INFO] GTDB search result was written to GCF_024643285.1_ASM2464328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:46,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:46,653] [INFO] DFAST_QC result json was written to GCF_024643285.1_ASM2464328v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:46,653] [INFO] DFAST_QC completed!
[2024-01-24 12:31:46,653] [INFO] Total running time: 0h1m41s