[2023-06-19 08:50:38,813] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:50:38,817] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:50:38,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference
[2023-06-19 08:50:40,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:50:40,289] [INFO] Task started: Prodigal
[2023-06-19 08:50:40,289] [INFO] Running command: gunzip -c /var/lib/cwl/stg29bf4767-73b8-461f-9629-9db908895a9d/GCA_018607835.1_ASM1860783v1_genomic.fna.gz | prodigal -d GCA_018607835.1_ASM1860783v1_genomic.fna/cds.fna -a GCA_018607835.1_ASM1860783v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:50:48,640] [INFO] Task succeeded: Prodigal
[2023-06-19 08:50:48,640] [INFO] Task started: HMMsearch
[2023-06-19 08:50:48,640] [INFO] Running command: hmmsearch --tblout GCA_018607835.1_ASM1860783v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference/reference_markers.hmm GCA_018607835.1_ASM1860783v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:50:48,948] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:50:48,950] [INFO] Found 6/6 markers.
[2023-06-19 08:50:49,006] [INFO] Query marker FASTA was written to GCA_018607835.1_ASM1860783v1_genomic.fna/markers.fasta
[2023-06-19 08:50:49,006] [INFO] Task started: Blastn
[2023-06-19 08:50:49,007] [INFO] Running command: blastn -query GCA_018607835.1_ASM1860783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference/reference_markers.fasta -out GCA_018607835.1_ASM1860783v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:49,730] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:49,735] [INFO] Selected 27 target genomes.
[2023-06-19 08:50:49,735] [INFO] Target genome list was writen to GCA_018607835.1_ASM1860783v1_genomic.fna/target_genomes.txt
[2023-06-19 08:50:49,741] [INFO] Task started: fastANI
[2023-06-19 08:50:49,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg29bf4767-73b8-461f-9629-9db908895a9d/GCA_018607835.1_ASM1860783v1_genomic.fna.gz --refList GCA_018607835.1_ASM1860783v1_genomic.fna/target_genomes.txt --output GCA_018607835.1_ASM1860783v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:51:10,162] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:10,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:51:10,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:51:10,179] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:51:10,180] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:51:10,180] [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
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.6947	57	773	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	76.5645	96	773	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	76.5585	66	773	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	76.4885	97	773	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	76.4884	80	773	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	76.488	76	773	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.4357	85	773	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.4016	55	773	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	76.3242	66	773	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	76.2965	55	773	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	76.294	55	773	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	76.284	54	773	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.2738	63	773	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	76.2285	68	773	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	76.1493	74	773	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	76.1388	80	773	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	76.0939	78	773	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	76.0682	70	773	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	75.9894	77	773	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:51:10,182] [INFO] DFAST Taxonomy check result was written to GCA_018607835.1_ASM1860783v1_genomic.fna/tc_result.tsv
[2023-06-19 08:51:10,183] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:51:10,183] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:51:10,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference/checkm_data
[2023-06-19 08:51:10,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:51:10,216] [INFO] Task started: CheckM
[2023-06-19 08:51:10,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607835.1_ASM1860783v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607835.1_ASM1860783v1_genomic.fna/checkm_input GCA_018607835.1_ASM1860783v1_genomic.fna/checkm_result
[2023-06-19 08:51:38,433] [INFO] Task succeeded: CheckM
[2023-06-19 08:51:38,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:51:38,464] [INFO] ===== Completeness check finished =====
[2023-06-19 08:51:38,464] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:51:38,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607835.1_ASM1860783v1_genomic.fna/markers.fasta)
[2023-06-19 08:51:38,465] [INFO] Task started: Blastn
[2023-06-19 08:51:38,465] [INFO] Running command: blastn -query GCA_018607835.1_ASM1860783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg747d6972-97ea-46cf-a5c4-9320dbbd400c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607835.1_ASM1860783v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:39,335] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:39,342] [INFO] Selected 27 target genomes.
[2023-06-19 08:51:39,343] [INFO] Target genome list was writen to GCA_018607835.1_ASM1860783v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:51:39,381] [INFO] Task started: fastANI
[2023-06-19 08:51:39,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg29bf4767-73b8-461f-9629-9db908895a9d/GCA_018607835.1_ASM1860783v1_genomic.fna.gz --refList GCA_018607835.1_ASM1860783v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607835.1_ASM1860783v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:51:54,454] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:54,481] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:51:54,481] [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
GCA_018607835.1	s__RS62 sp002340675	100.0	767	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	99.19	98.96	0.91	0.88	5	conclusive
GCA_000496475.1	s__RS62 sp000496475	77.3521	134	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RS62	95.0	98.53	98.53	0.95	0.95	2	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	77.1653	87	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	76.9539	102	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003241965.1	s__Hydrogenophaga sp003241965	76.7359	92	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063545.1	s__Limnohabitans sp003063545	76.7048	84	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798165.1	s__Rhodoferax sp017798165	76.6588	74	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886485.1	s__Limnohabitans sp903886485	76.6476	80	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCA_001795455.1	s__Rhodoferax sp001795455	76.5972	81	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	76.5953	82	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063475.1	s__Limnohabitans curvus	76.5645	96	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCF_000175235.1	s__Acidovorax delafieldii_B	76.5183	80	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111115.1	s__Giesbergeria anulus	76.4999	53	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096555.1	s__Giesbergeria sp003096555	76.494	69	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCF_001571145.1	s__Hydrogenophaga flava	76.4884	80	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778325.1	s__Limnohabitans sp002778325	76.4832	108	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828535.1	s__Curvibacter sp903828535	76.4407	69	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.0	99.64	99.54	0.96	0.96	4	-
GCA_016708345.1	s__Rhodoferax sp016708345	76.4398	60	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.29	99.29	0.95	0.95	2	-
GCA_903832625.1	s__Limnohabitans sp903832625	76.4244	83	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCA_001770955.1	s__Giesbergeria sp001770955	76.3896	51	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCA_016721925.1	s__JAABQG01 sp016721925	76.3537	79	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCA_002842215.1	s__Hydrogenophaga sp002842215	76.3286	94	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932145.1	s__Giesbergeria sp012932145	76.2695	71	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCA_012927445.1	s__Rhodoferax sp012927445	76.2375	68	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.76	98.76	0.94	0.94	2	-
GCF_003053545.1	s__Acidovorax sp003053545	76.2202	80	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_002127265.1	s__Hydrogenophaga sp002127265	76.1734	69	773	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:51:54,483] [INFO] GTDB search result was written to GCA_018607835.1_ASM1860783v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:51:54,484] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:51:54,489] [INFO] DFAST_QC result json was written to GCA_018607835.1_ASM1860783v1_genomic.fna/dqc_result.json
[2023-06-19 08:51:54,489] [INFO] DFAST_QC completed!
[2023-06-19 08:51:54,489] [INFO] Total running time: 0h1m16s