[2024-01-24 12:22:13,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:13,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:13,941] [INFO] DQC Reference Directory: /var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference
[2024-01-24 12:22:15,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,346] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg402d9920-d068-40f3-860d-fbac9cc6927f/GCF_002934635.1_ASM293463v1_genomic.fna.gz | prodigal -d GCF_002934635.1_ASM293463v1_genomic.fna/cds.fna -a GCF_002934635.1_ASM293463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:50,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:50,580] [INFO] Task started: HMMsearch
[2024-01-24 12:22:50,580] [INFO] Running command: hmmsearch --tblout GCF_002934635.1_ASM293463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference/reference_markers.hmm GCF_002934635.1_ASM293463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:51,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:51,074] [INFO] Found 6/6 markers.
[2024-01-24 12:22:51,125] [INFO] Query marker FASTA was written to GCF_002934635.1_ASM293463v1_genomic.fna/markers.fasta
[2024-01-24 12:22:51,125] [INFO] Task started: Blastn
[2024-01-24 12:22:51,125] [INFO] Running command: blastn -query GCF_002934635.1_ASM293463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference/reference_markers.fasta -out GCF_002934635.1_ASM293463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:51,753] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:51,758] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:51,758] [INFO] Target genome list was writen to GCF_002934635.1_ASM293463v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:51,771] [INFO] Task started: fastANI
[2024-01-24 12:22:51,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg402d9920-d068-40f3-860d-fbac9cc6927f/GCF_002934635.1_ASM293463v1_genomic.fna.gz --refList GCF_002934635.1_ASM293463v1_genomic.fna/target_genomes.txt --output GCF_002934635.1_ASM293463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:08,760] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:08,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:08,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:08,770] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:08,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:08,770] [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 indicus	strain=RK1	GCA_002934635.1	1477437	1477437	type	True	100.0	2034	2036	95	conclusive
Parapedobacter indicus	strain=RK1	GCA_900113765.1	1477437	1477437	type	True	99.9981	2031	2036	95	conclusive
Parapedobacter defluvii	strain=CGMCC 1.15342	GCA_014642075.1	2045106	2045106	type	True	80.7927	942	2036	95	below_threshold
Parapedobacter pyrenivorans	strain=CGMCC 1.12195	GCA_014636865.1	1305674	1305674	type	True	79.7873	534	2036	95	below_threshold
Sphingobacterium thalpophilum	strain=NCTC11429	GCA_901482695.1	259	259	type	True	78.4027	61	2036	95	below_threshold
Sphingobacterium thalpophilum	strain=DSM 11723	GCA_000686625.1	259	259	type	True	78.3778	61	2036	95	below_threshold
Parapedobacter koreensis	strain=Jip14	GCA_900109365.1	332977	332977	type	True	77.8931	356	2036	95	below_threshold
Parapedobacter composti	strain=DSM 22900	GCA_900112315.1	623281	623281	type	True	77.4953	223	2036	95	below_threshold
Parapedobacter luteus	strain=DSM 22899	GCA_900168055.1	623280	623280	type	True	77.436	294	2036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:08,772] [INFO] DFAST Taxonomy check result was written to GCF_002934635.1_ASM293463v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:08,773] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:08,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:08,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference/checkm_data
[2024-01-24 12:23:08,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:08,835] [INFO] Task started: CheckM
[2024-01-24 12:23:08,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934635.1_ASM293463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934635.1_ASM293463v1_genomic.fna/checkm_input GCF_002934635.1_ASM293463v1_genomic.fna/checkm_result
[2024-01-24 12:24:44,196] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:44,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:44,228] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:44,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:44,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934635.1_ASM293463v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:44,229] [INFO] Task started: Blastn
[2024-01-24 12:24:44,229] [INFO] Running command: blastn -query GCF_002934635.1_ASM293463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga04b4c33-eabf-42ee-948c-5a9f8780778f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934635.1_ASM293463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:45,011] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:45,016] [INFO] Selected 25 target genomes.
[2024-01-24 12:24:45,016] [INFO] Target genome list was writen to GCF_002934635.1_ASM293463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:45,035] [INFO] Task started: fastANI
[2024-01-24 12:24:45,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg402d9920-d068-40f3-860d-fbac9cc6927f/GCF_002934635.1_ASM293463v1_genomic.fna.gz --refList GCF_002934635.1_ASM293463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934635.1_ASM293463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:03,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:03,315] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:03,315] [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_900113765.1	s__Parapedobacter indicus	99.9981	2031	2036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014642075.1	s__Parapedobacter defluvii	80.8058	940	2036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636865.1	s__Parapedobacter pyrenivorans	79.8023	532	2036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901482695.1	s__Sphingobacterium thalpophilum	78.5545	58	2036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.60	99.20	0.96	0.93	3	-
GCF_900109365.1	s__Parapedobacter koreensis	77.9092	355	2036	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	77.4959	223	2036	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	77.4496	291	2036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	99.02	99.02	0.90	0.90	2	-
GCF_011030405.1	s__Sphingobacterium sp011030405	76.3032	55	2036	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:03,317] [INFO] GTDB search result was written to GCF_002934635.1_ASM293463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:03,317] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:03,320] [INFO] DFAST_QC result json was written to GCF_002934635.1_ASM293463v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:03,320] [INFO] DFAST_QC completed!
[2024-01-24 12:25:03,320] [INFO] Total running time: 0h2m49s