[2024-01-24 15:18:05,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference
[2024-01-24 15:18:07,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,531] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,532] [INFO] Running command: gunzip -c /var/lib/cwl/stg89148a31-b84d-409f-aede-59f9cad1e9e1/GCF_000739995.1_ASM73999v1_genomic.fna.gz | prodigal -d GCF_000739995.1_ASM73999v1_genomic.fna/cds.fna -a GCF_000739995.1_ASM73999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:19,321] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:19,322] [INFO] Task started: HMMsearch
[2024-01-24 15:18:19,322] [INFO] Running command: hmmsearch --tblout GCF_000739995.1_ASM73999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference/reference_markers.hmm GCF_000739995.1_ASM73999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:19,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:19,612] [INFO] Found 6/6 markers.
[2024-01-24 15:18:19,653] [INFO] Query marker FASTA was written to GCF_000739995.1_ASM73999v1_genomic.fna/markers.fasta
[2024-01-24 15:18:19,654] [INFO] Task started: Blastn
[2024-01-24 15:18:19,654] [INFO] Running command: blastn -query GCF_000739995.1_ASM73999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference/reference_markers.fasta -out GCF_000739995.1_ASM73999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:20,760] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:20,764] [INFO] Selected 21 target genomes.
[2024-01-24 15:18:20,764] [INFO] Target genome list was writen to GCF_000739995.1_ASM73999v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:20,794] [INFO] Task started: fastANI
[2024-01-24 15:18:20,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg89148a31-b84d-409f-aede-59f9cad1e9e1/GCF_000739995.1_ASM73999v1_genomic.fna.gz --refList GCF_000739995.1_ASM73999v1_genomic.fna/target_genomes.txt --output GCF_000739995.1_ASM73999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:39,847] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:39,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:39,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:39,872] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:39,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:39,873] [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_001298675.1	343013	343013	type	True	83.4235	718	1152	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	83.3913	719	1152	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	83.0465	719	1152	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	82.9971	435	1152	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	82.9251	689	1152	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	82.7914	646	1152	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	82.6728	716	1152	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	82.5779	698	1152	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	82.2166	682	1152	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.9512	706	1152	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.8296	724	1152	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.7885	620	1152	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	81.7511	628	1152	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	81.7172	666	1152	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	81.6585	703	1152	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.4885	631	1152	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	81.1316	590	1152	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	80.9615	673	1152	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.3791	503	1152	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	80.2999	595	1152	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	79.4802	531	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:39,875] [INFO] DFAST Taxonomy check result was written to GCF_000739995.1_ASM73999v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:39,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:39,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:39,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference/checkm_data
[2024-01-24 15:18:39,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:39,918] [INFO] Task started: CheckM
[2024-01-24 15:18:39,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739995.1_ASM73999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739995.1_ASM73999v1_genomic.fna/checkm_input GCF_000739995.1_ASM73999v1_genomic.fna/checkm_result
[2024-01-24 15:19:25,852] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:25,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:25,876] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:25,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:25,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739995.1_ASM73999v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:25,878] [INFO] Task started: Blastn
[2024-01-24 15:19:25,878] [INFO] Running command: blastn -query GCF_000739995.1_ASM73999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg318b4514-529c-466c-81e1-54a365078b81/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739995.1_ASM73999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:28,149] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:28,153] [INFO] Selected 17 target genomes.
[2024-01-24 15:19:28,154] [INFO] Target genome list was writen to GCF_000739995.1_ASM73999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:28,184] [INFO] Task started: fastANI
[2024-01-24 15:19:28,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg89148a31-b84d-409f-aede-59f9cad1e9e1/GCF_000739995.1_ASM73999v1_genomic.fna.gz --refList GCF_000739995.1_ASM73999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739995.1_ASM73999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:44,904] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:44,918] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:44,919] [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_000739995.1	s__Giesbergeria granuli	100.0	1150	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	conclusive
GCF_003604195.1	s__Giesbergeria lacusdiani	87.0786	853	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192425.1	s__Giesbergeria sp016192425	86.5208	809	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010020825.1	s__Giesbergeria sp010020825	86.2404	838	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCA_001770955.1	s__Giesbergeria sp001770955	84.8262	782	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCA_001725235.1	s__Acidovorax_C sp001725235	84.5463	769	1152	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_000204645.1	s__Alicycliphilus denitrificans	84.3902	778	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_000400995.2	s__MR-S7 sp000400995	84.0283	754	1152	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_014489595.1	s__Acidovorax_F monticola	83.9856	782	1152	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_001298675.1	s__Acidovorax_C caeni	83.4656	715	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	99.98	99.98	0.98	0.98	2	-
GCA_001724785.1	s__Giesbergeria sp001724785	83.1238	557	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011303755.1	s__Acidovorax_C sp011303755	83.0305	650	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	82.97	813	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240985.1	s__Alicycliphilus sp018240985	82.9472	616	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCF_003269065.1	s__Acidovorax_A anthurii	82.5996	697	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100305.1	s__Acidovorax_A citrulli	82.2243	681	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCA_001725255.1	s__Comamonas_C sp001725255	81.2342	613	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_C	95.0	98.57	95.76	0.95	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:44,921] [INFO] GTDB search result was written to GCF_000739995.1_ASM73999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:44,921] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:44,927] [INFO] DFAST_QC result json was written to GCF_000739995.1_ASM73999v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:44,927] [INFO] DFAST_QC completed!
[2024-01-24 15:19:44,927] [INFO] Total running time: 0h1m40s