[2023-06-30 14:54:12,325] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:54:12,328] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:54:12,328] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference
[2023-06-30 14:54:13,629] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:54:13,630] [INFO] Task started: Prodigal
[2023-06-30 14:54:13,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg9771b7a9-39aa-4773-ad85-3d32757cf9d9/GCA_024708985.1_ASM2470898v1_genomic.fna.gz | prodigal -d GCA_024708985.1_ASM2470898v1_genomic.fna/cds.fna -a GCA_024708985.1_ASM2470898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:23,571] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:23,571] [INFO] Task started: HMMsearch
[2023-06-30 14:54:23,571] [INFO] Running command: hmmsearch --tblout GCA_024708985.1_ASM2470898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference/reference_markers.hmm GCA_024708985.1_ASM2470898v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:23,952] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:23,954] [INFO] Found 6/6 markers.
[2023-06-30 14:54:23,996] [INFO] Query marker FASTA was written to GCA_024708985.1_ASM2470898v1_genomic.fna/markers.fasta
[2023-06-30 14:54:23,996] [INFO] Task started: Blastn
[2023-06-30 14:54:23,996] [INFO] Running command: blastn -query GCA_024708985.1_ASM2470898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference/reference_markers.fasta -out GCA_024708985.1_ASM2470898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:25,036] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:25,040] [INFO] Selected 28 target genomes.
[2023-06-30 14:54:25,041] [INFO] Target genome list was writen to GCA_024708985.1_ASM2470898v1_genomic.fna/target_genomes.txt
[2023-06-30 14:54:25,043] [INFO] Task started: fastANI
[2023-06-30 14:54:25,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg9771b7a9-39aa-4773-ad85-3d32757cf9d9/GCA_024708985.1_ASM2470898v1_genomic.fna.gz --refList GCA_024708985.1_ASM2470898v1_genomic.fna/target_genomes.txt --output GCA_024708985.1_ASM2470898v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:51,009] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:51,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:51,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:51,031] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:51,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:54:51,031] [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 wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.7108	590	776	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	82.431	508	776	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	82.3764	510	776	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	82.3438	511	776	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	82.3103	357	776	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	82.1474	568	776	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	81.8694	524	776	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.8567	540	776	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	81.6044	570	776	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	81.5833	569	776	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	81.5731	464	776	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	81.5471	550	776	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.5467	549	776	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	81.5428	553	776	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.4126	509	776	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.0505	543	776	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.7329	438	776	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.53	504	776	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	80.5252	472	776	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.2293	500	776	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	80.197	430	776	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	79.8151	445	776	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.7984	438	776	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	79.7365	414	776	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.4018	421	776	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.2495	368	776	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.2371	439	776	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	79.2291	411	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:54:51,033] [INFO] DFAST Taxonomy check result was written to GCA_024708985.1_ASM2470898v1_genomic.fna/tc_result.tsv
[2023-06-30 14:54:51,034] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:51,034] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:51,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference/checkm_data
[2023-06-30 14:54:51,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:51,075] [INFO] Task started: CheckM
[2023-06-30 14:54:51,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708985.1_ASM2470898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708985.1_ASM2470898v1_genomic.fna/checkm_input GCA_024708985.1_ASM2470898v1_genomic.fna/checkm_result
[2023-06-30 14:55:23,111] [INFO] Task succeeded: CheckM
[2023-06-30 14:55:23,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.85%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 14:55:23,138] [INFO] ===== Completeness check finished =====
[2023-06-30 14:55:23,138] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:55:23,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708985.1_ASM2470898v1_genomic.fna/markers.fasta)
[2023-06-30 14:55:23,139] [INFO] Task started: Blastn
[2023-06-30 14:55:23,139] [INFO] Running command: blastn -query GCA_024708985.1_ASM2470898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3e66bf2-a7c9-4d25-b0a1-1d2a783d0ec3/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708985.1_ASM2470898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:55:24,898] [INFO] Task succeeded: Blastn
[2023-06-30 14:55:24,904] [INFO] Selected 22 target genomes.
[2023-06-30 14:55:24,904] [INFO] Target genome list was writen to GCA_024708985.1_ASM2470898v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:55:24,917] [INFO] Task started: fastANI
[2023-06-30 14:55:24,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg9771b7a9-39aa-4773-ad85-3d32757cf9d9/GCA_024708985.1_ASM2470898v1_genomic.fna.gz --refList GCA_024708985.1_ASM2470898v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708985.1_ASM2470898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:55:43,085] [INFO] Task succeeded: fastANI
[2023-06-30 14:55:43,115] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:55:43,115] [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_003755025.1	s__Diaphorobacter nitroreducens	98.2242	742	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	conclusive
GCF_000204645.1	s__Alicycliphilus denitrificans	85.4927	626	776	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	85.2039	634	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCA_018241405.1	s__Alicycliphilus sp018241405	83.8704	574	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCA_002434305.1	s__Pulveribacter sp002434305	83.5257	594	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCA_018242005.1	s__Alicycliphilus sp018242005	83.4853	543	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240985.1	s__Alicycliphilus sp018240985	83.3019	511	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCA_001725235.1	s__Acidovorax_C sp001725235	83.184	555	776	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_003013695.1	s__Pulveribacter suum	83.1211	583	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489595.1	s__Acidovorax_F monticola	83.0796	611	776	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_003604195.1	s__Giesbergeria lacusdiani	82.6976	518	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113035.1	s__Acidovorax_A wautersii	82.6921	592	776	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_001424265.1	s__Acidovorax_A sp001424265	82.2345	568	776	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_003269065.1	s__Acidovorax_A anthurii	82.1566	567	776	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	81.8903	537	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
GCF_017811175.1	s__Melaminivora_A jejuensis	81.8735	524	776	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_014637085.1	s__Comamonas phosphati	81.6081	462	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176855.2	s__Acidovorax_A avenae	81.5589	571	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCA_005503335.1	s__SCMQ01 sp005503335	80.9409	443	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCF_900461435.1	s__Comamonas terrigena	80.551	470	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCA_017998575.1	s__JAGOCV01 sp017998575	79.3792	327	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAGOCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207855.1	s__Comamonas odontotermitis	79.1749	388	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-30 14:55:43,117] [INFO] GTDB search result was written to GCA_024708985.1_ASM2470898v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:55:43,118] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:55:43,123] [INFO] DFAST_QC result json was written to GCA_024708985.1_ASM2470898v1_genomic.fna/dqc_result.json
[2023-06-30 14:55:43,123] [INFO] DFAST_QC completed!
[2023-06-30 14:55:43,123] [INFO] Total running time: 0h1m31s