[2024-01-24 14:18:59,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:18:59,319] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:18:59,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference
[2024-01-24 14:19:00,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:00,581] [INFO] Task started: Prodigal
[2024-01-24 14:19:00,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b9e0e4e-93fb-4d6b-a4df-4461ffb73f89/GCF_003008575.1_ASM300857v1_genomic.fna.gz | prodigal -d GCF_003008575.1_ASM300857v1_genomic.fna/cds.fna -a GCF_003008575.1_ASM300857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:13,777] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:13,778] [INFO] Task started: HMMsearch
[2024-01-24 14:19:13,778] [INFO] Running command: hmmsearch --tblout GCF_003008575.1_ASM300857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference/reference_markers.hmm GCF_003008575.1_ASM300857v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:14,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:14,103] [INFO] Found 6/6 markers.
[2024-01-24 14:19:14,137] [INFO] Query marker FASTA was written to GCF_003008575.1_ASM300857v1_genomic.fna/markers.fasta
[2024-01-24 14:19:14,137] [INFO] Task started: Blastn
[2024-01-24 14:19:14,137] [INFO] Running command: blastn -query GCF_003008575.1_ASM300857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference/reference_markers.fasta -out GCF_003008575.1_ASM300857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:15,301] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:15,311] [INFO] Selected 16 target genomes.
[2024-01-24 14:19:15,311] [INFO] Target genome list was writen to GCF_003008575.1_ASM300857v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:15,371] [INFO] Task started: fastANI
[2024-01-24 14:19:15,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b9e0e4e-93fb-4d6b-a4df-4461ffb73f89/GCF_003008575.1_ASM300857v1_genomic.fna.gz --refList GCF_003008575.1_ASM300857v1_genomic.fna/target_genomes.txt --output GCF_003008575.1_ASM300857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:33,443] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:33,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:33,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:33,460] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:33,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:33,460] [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	87.7428	957	1251	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	85.7622	514	1251	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	85.6661	794	1251	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.563	772	1251	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	81.7449	683	1251	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.5836	715	1251	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.3605	714	1251	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.3331	673	1251	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.3224	723	1251	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.9117	695	1251	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.791	742	1251	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.6221	602	1251	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.4888	673	1251	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.272	674	1251	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.2549	619	1251	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.0284	556	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:33,462] [INFO] DFAST Taxonomy check result was written to GCF_003008575.1_ASM300857v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:33,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:33,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:33,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference/checkm_data
[2024-01-24 14:19:33,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:33,507] [INFO] Task started: CheckM
[2024-01-24 14:19:33,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003008575.1_ASM300857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003008575.1_ASM300857v1_genomic.fna/checkm_input GCF_003008575.1_ASM300857v1_genomic.fna/checkm_result
[2024-01-24 14:20:23,182] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:23,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:23,203] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:23,204] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:23,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003008575.1_ASM300857v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:23,205] [INFO] Task started: Blastn
[2024-01-24 14:20:23,205] [INFO] Running command: blastn -query GCF_003008575.1_ASM300857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63172b92-2857-4366-85cc-af4fd57662c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003008575.1_ASM300857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,673] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,677] [INFO] Selected 7 target genomes.
[2024-01-24 14:20:25,677] [INFO] Target genome list was writen to GCF_003008575.1_ASM300857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:25,688] [INFO] Task started: fastANI
[2024-01-24 14:20:25,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b9e0e4e-93fb-4d6b-a4df-4461ffb73f89/GCF_003008575.1_ASM300857v1_genomic.fna.gz --refList GCF_003008575.1_ASM300857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003008575.1_ASM300857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:33,034] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:33,042] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:33,042] [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_003008575.1	s__Melaminivora_A sp003008575	100.0	1251	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_017811175.1	s__Melaminivora_A jejuensis	87.7811	952	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	87.1023	891	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	86.8293	889	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	86.7507	880	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	85.7642	513	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	83.2414	786	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:33,044] [INFO] GTDB search result was written to GCF_003008575.1_ASM300857v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:33,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:33,047] [INFO] DFAST_QC result json was written to GCF_003008575.1_ASM300857v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:33,047] [INFO] DFAST_QC completed!
[2024-01-24 14:20:33,047] [INFO] Total running time: 0h1m34s