[2024-01-24 14:19:59,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,860] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference
[2024-01-24 14:20:01,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,457] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,457] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d79ee21-9a2c-41f0-8750-62da7a044b35/GCF_010686705.1_ASM1068670v1_genomic.fna.gz | prodigal -d GCF_010686705.1_ASM1068670v1_genomic.fna/cds.fna -a GCF_010686705.1_ASM1068670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:13,986] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:13,986] [INFO] Task started: HMMsearch
[2024-01-24 14:20:13,986] [INFO] Running command: hmmsearch --tblout GCF_010686705.1_ASM1068670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference/reference_markers.hmm GCF_010686705.1_ASM1068670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:14,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:14,289] [INFO] Found 6/6 markers.
[2024-01-24 14:20:14,328] [INFO] Query marker FASTA was written to GCF_010686705.1_ASM1068670v1_genomic.fna/markers.fasta
[2024-01-24 14:20:14,329] [INFO] Task started: Blastn
[2024-01-24 14:20:14,329] [INFO] Running command: blastn -query GCF_010686705.1_ASM1068670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference/reference_markers.fasta -out GCF_010686705.1_ASM1068670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:15,586] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:15,590] [INFO] Selected 17 target genomes.
[2024-01-24 14:20:15,590] [INFO] Target genome list was writen to GCF_010686705.1_ASM1068670v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:15,607] [INFO] Task started: fastANI
[2024-01-24 14:20:15,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d79ee21-9a2c-41f0-8750-62da7a044b35/GCF_010686705.1_ASM1068670v1_genomic.fna.gz --refList GCF_010686705.1_ASM1068670v1_genomic.fna/target_genomes.txt --output GCF_010686705.1_ASM1068670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:27,261] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:27,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:27,276] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:27,277] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:27,277] [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
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	80.5185	455	1347	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	80.459	657	1347	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	80.3689	610	1347	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	80.337	604	1347	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	80.2891	575	1347	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	79.3175	343	1347	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	79.1451	308	1347	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	78.9026	438	1347	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.7136	344	1347	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.7047	406	1347	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	78.7	334	1347	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	78.6927	338	1347	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.6796	455	1347	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.6628	369	1347	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.5972	395	1347	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.5004	334	1347	95	below_threshold
Labedella populi	strain=8H24J-4-2	GCA_004078655.1	2498850	2498850	type	True	78.1697	294	1347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,278] [INFO] DFAST Taxonomy check result was written to GCF_010686705.1_ASM1068670v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:27,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:27,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:27,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference/checkm_data
[2024-01-24 14:20:27,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:27,323] [INFO] Task started: CheckM
[2024-01-24 14:20:27,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010686705.1_ASM1068670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010686705.1_ASM1068670v1_genomic.fna/checkm_input GCF_010686705.1_ASM1068670v1_genomic.fna/checkm_result
[2024-01-24 14:21:08,853] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:08,855] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,876] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:08,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:08,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010686705.1_ASM1068670v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:08,877] [INFO] Task started: Blastn
[2024-01-24 14:21:08,878] [INFO] Running command: blastn -query GCF_010686705.1_ASM1068670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd06047d-9e1c-454f-bd29-479a5adadfe7/dqc_reference/reference_markers_gtdb.fasta -out GCF_010686705.1_ASM1068670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:10,745] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:10,749] [INFO] Selected 15 target genomes.
[2024-01-24 14:21:10,750] [INFO] Target genome list was writen to GCF_010686705.1_ASM1068670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:10,766] [INFO] Task started: fastANI
[2024-01-24 14:21:10,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d79ee21-9a2c-41f0-8750-62da7a044b35/GCF_010686705.1_ASM1068670v1_genomic.fna.gz --refList GCF_010686705.1_ASM1068670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010686705.1_ASM1068670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:23,241] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:23,257] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:23,258] [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_010686705.1	s__Diaminobutyricibacter tongyongensis	100.0	1346	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012317045.1	s__Leifsonia sp002105485	80.8928	642	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.03	98.03	0.91	0.91	2	-
GCF_001428745.1	s__Leifsonia sp001428745	80.833	626	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217625.1	s__Leifsonia shinshuensis_A	80.456	643	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410375.1	s__Leifsonia shinshuensis	80.4444	659	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190775.1	s__Leifsonia aquatica	80.3523	602	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCA_001898805.1	s__Leifsonia sp001898805	80.3096	595	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647635.1	s__Leifsonia xyli_A	80.3058	605	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408745.1	s__Leifsonia soli	80.3032	574	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.25	98.25	0.89	0.89	2	-
GCF_001423695.1	s__Leifsonia sp001423695	80.2988	638	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664105.1	s__Leifsonia sp003664105	80.2735	607	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565305.1	s__Leifsonia sp017565305	80.262	611	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	97.25	97.25	0.89	0.89	2	-
GCF_000633535.1	s__Leifsonia aquatica_A	80.1663	586	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765225.1	s__Leifsonia sp009765225	79.9956	559	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797855.1	s__Compostimonas suwonensis	79.2372	434	1347	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:23,259] [INFO] GTDB search result was written to GCF_010686705.1_ASM1068670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:23,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:23,265] [INFO] DFAST_QC result json was written to GCF_010686705.1_ASM1068670v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:23,265] [INFO] DFAST_QC completed!
[2024-01-24 14:21:23,266] [INFO] Total running time: 0h1m23s