[2024-01-25 19:11:35,439] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:35,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:35,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference
[2024-01-25 19:11:36,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:36,595] [INFO] Task started: Prodigal
[2024-01-25 19:11:36,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgabc46822-4d13-4170-abe0-4c8b6309af11/GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna.gz | prodigal -d GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/cds.fna -a GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:52,728] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:52,729] [INFO] Task started: HMMsearch
[2024-01-25 19:11:52,729] [INFO] Running command: hmmsearch --tblout GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference/reference_markers.hmm GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:53,037] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:53,038] [INFO] Found 6/6 markers.
[2024-01-25 19:11:53,096] [INFO] Query marker FASTA was written to GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/markers.fasta
[2024-01-25 19:11:53,096] [INFO] Task started: Blastn
[2024-01-25 19:11:53,096] [INFO] Running command: blastn -query GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference/reference_markers.fasta -out GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:53,683] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:53,689] [INFO] Selected 11 target genomes.
[2024-01-25 19:11:53,689] [INFO] Target genome list was writen to GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/target_genomes.txt
[2024-01-25 19:11:53,701] [INFO] Task started: fastANI
[2024-01-25 19:11:53,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc46822-4d13-4170-abe0-4c8b6309af11/GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna.gz --refList GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/target_genomes.txt --output GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:09,062] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:09,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:09,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:09,071] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:09,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:09,071] [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
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	100.0	1735	1746	95	conclusive
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	92.1421	1234	1746	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	92.0855	1244	1746	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	89.0545	1218	1746	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	86.6036	1116	1746	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	86.5775	1130	1746	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	84.1763	1059	1746	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	83.1586	1005	1746	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.9769	959	1746	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.9702	94	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:09,072] [INFO] DFAST Taxonomy check result was written to GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/tc_result.tsv
[2024-01-25 19:12:09,073] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:09,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:09,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference/checkm_data
[2024-01-25 19:12:09,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:09,129] [INFO] Task started: CheckM
[2024-01-25 19:12:09,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/checkm_input GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/checkm_result
[2024-01-25 19:12:55,891] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:55,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:55,912] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:55,912] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:55,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/markers.fasta)
[2024-01-25 19:12:55,913] [INFO] Task started: Blastn
[2024-01-25 19:12:55,913] [INFO] Running command: blastn -query GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2f7f78-182d-4199-b214-008731c3581d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:56,734] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:56,737] [INFO] Selected 12 target genomes.
[2024-01-25 19:12:56,737] [INFO] Target genome list was writen to GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:56,758] [INFO] Task started: fastANI
[2024-01-25 19:12:56,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc46822-4d13-4170-abe0-4c8b6309af11/GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna.gz --refList GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/target_genomes_gtdb.txt --output GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:15,308] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:15,317] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:15,317] [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_000708285.2	s__Pedobacter borealis	100.0	1735	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018613605.1	s__Pedobacter sp018613605	93.7393	1224	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_004310665.1	s__Pedobacter kyonggii	92.1367	1235	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	92.0733	1245	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387415.1	s__Pedobacter sp003387415	91.197	1194	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	89.5976	1250	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331735.1	s__Pedobacter sp004331735	89.0364	1220	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692875.1	s__Pedobacter sp011759615	88.4277	1191	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCA_002151545.1	s__Pedobacter sp002151545	88.1944	1237	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664035.1	s__Pedobacter alluvionis	86.6015	1116	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004342125.1	s__Pedobacter sp004342125	86.4892	1125	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_001421515.1	s__Pedobacter sp001421515	83.8634	1045	1746	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:15,319] [INFO] GTDB search result was written to GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:15,319] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:15,323] [INFO] DFAST_QC result json was written to GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626_genomic.fna/dqc_result.json
[2024-01-25 19:13:15,323] [INFO] DFAST_QC completed!
[2024-01-25 19:13:15,323] [INFO] Total running time: 0h1m40s