[2024-01-25 18:41:35,452] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:35,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:35,453] [INFO] DQC Reference Directory: /var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference
[2024-01-25 18:41:36,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:36,615] [INFO] Task started: Prodigal
[2024-01-25 18:41:36,616] [INFO] Running command: gunzip -c /var/lib/cwl/stgc14201ca-7b9c-44a3-976a-14533538f2fc/GCF_017811175.1_ASM1781117v1_genomic.fna.gz | prodigal -d GCF_017811175.1_ASM1781117v1_genomic.fna/cds.fna -a GCF_017811175.1_ASM1781117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:47,781] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:47,781] [INFO] Task started: HMMsearch
[2024-01-25 18:41:47,781] [INFO] Running command: hmmsearch --tblout GCF_017811175.1_ASM1781117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference/reference_markers.hmm GCF_017811175.1_ASM1781117v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:48,029] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:48,030] [INFO] Found 6/6 markers.
[2024-01-25 18:41:48,075] [INFO] Query marker FASTA was written to GCF_017811175.1_ASM1781117v1_genomic.fna/markers.fasta
[2024-01-25 18:41:48,076] [INFO] Task started: Blastn
[2024-01-25 18:41:48,076] [INFO] Running command: blastn -query GCF_017811175.1_ASM1781117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference/reference_markers.fasta -out GCF_017811175.1_ASM1781117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:49,143] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:49,145] [INFO] Selected 20 target genomes.
[2024-01-25 18:41:49,146] [INFO] Target genome list was writen to GCF_017811175.1_ASM1781117v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:49,151] [INFO] Task started: fastANI
[2024-01-25 18:41:49,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgc14201ca-7b9c-44a3-976a-14533538f2fc/GCF_017811175.1_ASM1781117v1_genomic.fna.gz --refList GCF_017811175.1_ASM1781117v1_genomic.fna/target_genomes.txt --output GCF_017811175.1_ASM1781117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:10,886] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:10,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:10,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:10,898] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:10,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:10,898] [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
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	100.0	1249	1251	95	conclusive
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	85.6389	520	1251	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	85.3877	803	1251	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.9305	743	1251	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	81.8359	694	1251	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	81.8085	692	1251	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.4471	748	1251	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	81.2769	739	1251	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	81.1587	636	1251	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.1102	687	1251	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.0714	678	1251	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	80.9981	658	1251	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.4189	606	1251	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.1671	685	1251	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.9932	643	1251	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.9291	591	1251	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.9258	652	1251	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	79.888	585	1251	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.5453	529	1251	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.4638	563	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:10,900] [INFO] DFAST Taxonomy check result was written to GCF_017811175.1_ASM1781117v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:10,900] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:10,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:10,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference/checkm_data
[2024-01-25 18:42:10,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:10,939] [INFO] Task started: CheckM
[2024-01-25 18:42:10,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017811175.1_ASM1781117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017811175.1_ASM1781117v1_genomic.fna/checkm_input GCF_017811175.1_ASM1781117v1_genomic.fna/checkm_result
[2024-01-25 18:43:14,097] [INFO] Task succeeded: CheckM
[2024-01-25 18:43:14,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:43:14,117] [INFO] ===== Completeness check finished =====
[2024-01-25 18:43:14,118] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:43:14,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017811175.1_ASM1781117v1_genomic.fna/markers.fasta)
[2024-01-25 18:43:14,119] [INFO] Task started: Blastn
[2024-01-25 18:43:14,119] [INFO] Running command: blastn -query GCF_017811175.1_ASM1781117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga598bc0c-9a98-4368-9c67-f2795f8699fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_017811175.1_ASM1781117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:16,340] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:16,344] [INFO] Selected 8 target genomes.
[2024-01-25 18:43:16,344] [INFO] Target genome list was writen to GCF_017811175.1_ASM1781117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:43:16,348] [INFO] Task started: fastANI
[2024-01-25 18:43:16,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgc14201ca-7b9c-44a3-976a-14533538f2fc/GCF_017811175.1_ASM1781117v1_genomic.fna.gz --refList GCF_017811175.1_ASM1781117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017811175.1_ASM1781117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:24,895] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:24,901] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:24,901] [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_017811175.1	s__Melaminivora_A jejuensis	100.0	1249	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003008575.1	s__Melaminivora_A sp003008575	87.8537	934	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013695.1	s__Pulveribacter suum	86.2385	867	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434305.1	s__Pulveribacter sp002434305	86.188	847	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	85.9585	862	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282995.1	s__Melaminivora alkalimesophila	85.6135	521	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	-
GCF_000400995.2	s__MR-S7 sp000400995	83.3131	802	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_003269065.1	s__Acidovorax_A anthurii	81.11	689	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:24,902] [INFO] GTDB search result was written to GCF_017811175.1_ASM1781117v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:24,903] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:24,906] [INFO] DFAST_QC result json was written to GCF_017811175.1_ASM1781117v1_genomic.fna/dqc_result.json
[2024-01-25 18:43:24,906] [INFO] DFAST_QC completed!
[2024-01-25 18:43:24,906] [INFO] Total running time: 0h1m49s