[2024-01-24 13:57:00,946] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,953] [INFO] DQC Reference Directory: /var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference
[2024-01-24 13:57:02,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,292] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg29436b94-b601-4db7-92d5-b67d70ed288c/GCF_003604195.1_ASM360419v1_genomic.fna.gz | prodigal -d GCF_003604195.1_ASM360419v1_genomic.fna/cds.fna -a GCF_003604195.1_ASM360419v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:15,542] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:15,542] [INFO] Task started: HMMsearch
[2024-01-24 13:57:15,542] [INFO] Running command: hmmsearch --tblout GCF_003604195.1_ASM360419v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference/reference_markers.hmm GCF_003604195.1_ASM360419v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:15,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:15,889] [INFO] Found 6/6 markers.
[2024-01-24 13:57:15,923] [INFO] Query marker FASTA was written to GCF_003604195.1_ASM360419v1_genomic.fna/markers.fasta
[2024-01-24 13:57:15,924] [INFO] Task started: Blastn
[2024-01-24 13:57:15,924] [INFO] Running command: blastn -query GCF_003604195.1_ASM360419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference/reference_markers.fasta -out GCF_003604195.1_ASM360419v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:17,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:17,007] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:17,007] [INFO] Target genome list was writen to GCF_003604195.1_ASM360419v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:17,017] [INFO] Task started: fastANI
[2024-01-24 13:57:17,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg29436b94-b601-4db7-92d5-b67d70ed288c/GCF_003604195.1_ASM360419v1_genomic.fna.gz --refList GCF_003604195.1_ASM360419v1_genomic.fna/target_genomes.txt --output GCF_003604195.1_ASM360419v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:43,856] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:43,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:43,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:43,878] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:43,878] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:43,878] [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 soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	83.8746	752	1215	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	83.6054	750	1215	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	83.4245	859	1215	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	83.2497	782	1215	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	83.1009	712	1215	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	83.0974	753	1215	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	83.0494	712	1215	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	82.9297	837	1215	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	82.7524	817	1215	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	82.7125	844	1215	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	82.593	677	1215	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	82.5114	740	1215	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	82.4975	749	1215	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	82.4501	681	1215	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	82.3138	736	1215	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	82.3033	728	1215	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	82.1527	755	1215	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	82.0346	734	1215	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.7306	618	1215	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	81.4273	710	1215	95	below_threshold
Verminephrobacter aporrectodeae subsp. tuberculatae	strain=At4	GCA_000193225.2	1110392	1110389	type	True	81.251	459	1215	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.0294	624	1215	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	80.9899	719	1215	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.891	619	1215	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.4501	641	1215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:43,880] [INFO] DFAST Taxonomy check result was written to GCF_003604195.1_ASM360419v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:43,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:43,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:43,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference/checkm_data
[2024-01-24 13:57:43,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:43,920] [INFO] Task started: CheckM
[2024-01-24 13:57:43,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003604195.1_ASM360419v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003604195.1_ASM360419v1_genomic.fna/checkm_input GCF_003604195.1_ASM360419v1_genomic.fna/checkm_result
[2024-01-24 13:58:30,956] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:30,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:30,980] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:30,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:30,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003604195.1_ASM360419v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:30,981] [INFO] Task started: Blastn
[2024-01-24 13:58:30,981] [INFO] Running command: blastn -query GCF_003604195.1_ASM360419v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge326bf19-bc0a-4b75-8d03-1814559ee158/dqc_reference/reference_markers_gtdb.fasta -out GCF_003604195.1_ASM360419v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:33,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:33,318] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:33,319] [INFO] Target genome list was writen to GCF_003604195.1_ASM360419v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:33,334] [INFO] Task started: fastANI
[2024-01-24 13:58:33,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg29436b94-b601-4db7-92d5-b67d70ed288c/GCF_003604195.1_ASM360419v1_genomic.fna.gz --refList GCF_003604195.1_ASM360419v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003604195.1_ASM360419v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:55,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:55,065] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:55,065] [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_003604195.1	s__Giesbergeria lacusdiani	100.0	1215	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001770955.1	s__Giesbergeria sp001770955	87.9437	914	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_000739995.1	s__Giesbergeria granuli	86.9464	873	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_010020825.1	s__Giesbergeria sp010020825	86.5821	909	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCA_016192425.1	s__Giesbergeria sp016192425	86.113	847	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	84.264	834	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_F	95.0	97.51	97.51	0.93	0.93	2	-
GCA_001725235.1	s__Acidovorax_C sp001725235	84.2167	782	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCA_019218755.1	s__Acidovorax sp019218755	84.0481	861	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_012932145.1	s__Giesbergeria sp012932145	83.9223	772	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_000204645.1	s__Alicycliphilus denitrificans	83.859	796	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCF_003053545.1	s__Acidovorax sp003053545	83.8362	871	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_014207955.1	s__Acidovorax soli_A	83.8345	883	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428665.1	s__Acidovorax sp001428665	83.7303	855	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
GCF_003852545.1	s__Acidovorax sp003852545	83.7081	881	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724785.1	s__Giesbergeria sp001724785	83.5239	569	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019219095.1	s__Acidovorax sp019219095	83.2896	843	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269065.1	s__Acidovorax_A anthurii	83.1192	751	1215	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_004341365.1	s__Giesbergeria metamorpha	82.495	678	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
GCA_017998575.1	s__JAGOCV01 sp017998575	80.4672	466	1215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:55,067] [INFO] GTDB search result was written to GCF_003604195.1_ASM360419v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:55,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:55,074] [INFO] DFAST_QC result json was written to GCF_003604195.1_ASM360419v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:55,074] [INFO] DFAST_QC completed!
[2024-01-24 13:58:55,074] [INFO] Total running time: 0h1m54s