[2024-01-24 13:40:34,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference
[2024-01-24 13:40:35,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,452] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,452] [INFO] Running command: gunzip -c /var/lib/cwl/stg59019f59-aff6-4427-aec8-589ba7ee0aca/GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/cds.fna -a GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,953] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,954] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,954] [INFO] Running command: hmmsearch --tblout GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference/reference_markers.hmm GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:50,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:50,297] [INFO] Found 6/6 markers.
[2024-01-24 13:40:50,336] [INFO] Query marker FASTA was written to GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:50,336] [INFO] Task started: Blastn
[2024-01-24 13:40:50,336] [INFO] Running command: blastn -query GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference/reference_markers.fasta -out GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:51,421] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:51,424] [INFO] Selected 21 target genomes.
[2024-01-24 13:40:51,424] [INFO] Target genome list was writen to GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:51,430] [INFO] Task started: fastANI
[2024-01-24 13:40:51,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg59019f59-aff6-4427-aec8-589ba7ee0aca/GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna.gz --refList GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,903] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,921] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:13,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,921] [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
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	100.0	1319	1325	95	conclusive
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	99.9818	1295	1325	95	conclusive
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.0911	735	1325	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	81.8396	432	1325	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.6343	706	1325	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	81.5888	638	1325	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.3935	694	1325	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.389	688	1325	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	81.3108	709	1325	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.3097	629	1325	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.2798	684	1325	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.247	596	1325	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.2429	742	1325	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	81.2309	734	1325	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.1619	702	1325	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	81.1381	692	1325	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	80.913	692	1325	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.28	574	1325	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.8753	526	1325	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.6402	527	1325	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.4198	543	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,923] [INFO] DFAST Taxonomy check result was written to GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference/checkm_data
[2024-01-24 13:41:13,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,981] [INFO] Task started: CheckM
[2024-01-24 13:41:13,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/checkm_input GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:42:01,774] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:01,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:01,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:42:01,799] [INFO] Task started: Blastn
[2024-01-24 13:42:01,799] [INFO] Running command: blastn -query GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f93656-30d8-4455-b8f5-7cdebd4e53d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:03,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:03,940] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:03,940] [INFO] Target genome list was writen to GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:03,959] [INFO] Task started: fastANI
[2024-01-24 13:42:03,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg59019f59-aff6-4427-aec8-589ba7ee0aca/GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna.gz --refList GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:17,703] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:17,716] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:17,716] [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_001298675.1	s__Acidovorax_C caeni	99.9818	1295	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCA_001725235.1	s__Acidovorax_C sp001725235	91.8002	981	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_014489595.1	s__Acidovorax_F monticola	83.6323	818	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCF_000400995.2	s__MR-S7 sp000400995	83.5818	803	1325	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_000739995.1	s__Giesbergeria granuli	83.5445	699	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_000204645.1	s__Alicycliphilus denitrificans	83.271	785	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_011303755.1	s__Acidovorax_C sp011303755	83.017	717	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	82.9832	727	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCF_014207955.1	s__Acidovorax soli_A	81.7161	782	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571325.1	s__Comamonas tsuruhatensis	81.3322	728	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCF_013363755.1	s__Comamonas antarcticus	80.7165	622	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422365.1	s__Pseudorhodoferax sp001422365	80.024	648	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorhodoferax	95.0	98.81	98.81	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:17,717] [INFO] GTDB search result was written to GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:17,718] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:17,722] [INFO] DFAST_QC result json was written to GCF_900116825.1_IMG-taxon_2634166357_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:17,722] [INFO] DFAST_QC completed!
[2024-01-24 13:42:17,722] [INFO] Total running time: 0h1m44s