[2024-01-24 15:18:38,796] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,799] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference
[2024-01-24 15:18:40,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,101] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,101] [INFO] Running command: gunzip -c /var/lib/cwl/stg02e65d00-9e85-44f4-9b72-5f2fdead0aaa/GCF_003013695.1_ASM301369v1_genomic.fna.gz | prodigal -d GCF_003013695.1_ASM301369v1_genomic.fna/cds.fna -a GCF_003013695.1_ASM301369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,801] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,802] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,802] [INFO] Running command: hmmsearch --tblout GCF_003013695.1_ASM301369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference/reference_markers.hmm GCF_003013695.1_ASM301369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:52,078] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:52,079] [INFO] Found 6/6 markers.
[2024-01-24 15:18:52,110] [INFO] Query marker FASTA was written to GCF_003013695.1_ASM301369v1_genomic.fna/markers.fasta
[2024-01-24 15:18:52,110] [INFO] Task started: Blastn
[2024-01-24 15:18:52,110] [INFO] Running command: blastn -query GCF_003013695.1_ASM301369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference/reference_markers.fasta -out GCF_003013695.1_ASM301369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:53,187] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:53,190] [INFO] Selected 17 target genomes.
[2024-01-24 15:18:53,190] [INFO] Target genome list was writen to GCF_003013695.1_ASM301369v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:53,193] [INFO] Task started: fastANI
[2024-01-24 15:18:53,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg02e65d00-9e85-44f4-9b72-5f2fdead0aaa/GCF_003013695.1_ASM301369v1_genomic.fna.gz --refList GCF_003013695.1_ASM301369v1_genomic.fna/target_genomes.txt --output GCF_003013695.1_ASM301369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:11,533] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:11,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:11,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:11,547] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:11,547] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:11,548] [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	86.3055	855	1119	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	85.945	513	1119	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	85.8843	796	1119	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	83.0796	802	1119	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	82.419	701	1119	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	82.3751	713	1119	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	82.1695	734	1119	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	82.0869	748	1119	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.9634	761	1119	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.9293	738	1119	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	81.9242	682	1119	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	81.0826	717	1119	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.8505	595	1119	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	80.8356	599	1119	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.4601	614	1119	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.2493	550	1119	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.7188	598	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:11,549] [INFO] DFAST Taxonomy check result was written to GCF_003013695.1_ASM301369v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:11,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:11,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:11,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference/checkm_data
[2024-01-24 15:19:11,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:11,585] [INFO] Task started: CheckM
[2024-01-24 15:19:11,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003013695.1_ASM301369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003013695.1_ASM301369v1_genomic.fna/checkm_input GCF_003013695.1_ASM301369v1_genomic.fna/checkm_result
[2024-01-24 15:19:54,599] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:54,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:54,624] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:54,624] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:54,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003013695.1_ASM301369v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:54,625] [INFO] Task started: Blastn
[2024-01-24 15:19:54,625] [INFO] Running command: blastn -query GCF_003013695.1_ASM301369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeba24a66-ea06-4911-9053-aa44f0c7654e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003013695.1_ASM301369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:56,803] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:56,807] [INFO] Selected 10 target genomes.
[2024-01-24 15:19:56,808] [INFO] Target genome list was writen to GCF_003013695.1_ASM301369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:56,816] [INFO] Task started: fastANI
[2024-01-24 15:19:56,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg02e65d00-9e85-44f4-9b72-5f2fdead0aaa/GCF_003013695.1_ASM301369v1_genomic.fna.gz --refList GCF_003013695.1_ASM301369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003013695.1_ASM301369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:07,868] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:07,884] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:07,884] [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_003013695.1	s__Pulveribacter suum	100.0	1119	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002434305.1	s__Pulveribacter sp002434305	91.3577	970	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCF_003008575.1	s__Melaminivora_A sp003008575	87.1354	887	1119	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_900103645.1	s__Oryzisolibacter propanilivorax	86.7211	885	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811175.1	s__Melaminivora_A jejuensis	86.301	857	1119	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_000282995.1	s__Melaminivora alkalimesophila	85.9851	511	1119	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	85.0693	855	1119	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_000204645.1	s__Alicycliphilus denitrificans	84.881	843	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	84.1246	816	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCA_018240985.1	s__Alicycliphilus sp018240985	83.4971	680	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:07,886] [INFO] GTDB search result was written to GCF_003013695.1_ASM301369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:07,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:07,890] [INFO] DFAST_QC result json was written to GCF_003013695.1_ASM301369v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:07,890] [INFO] DFAST_QC completed!
[2024-01-24 15:20:07,890] [INFO] Total running time: 0h1m29s