[2023-06-29 05:05:03,941] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:05:03,943] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:05:03,943] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference
[2023-06-29 05:05:06,289] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:05:06,290] [INFO] Task started: Prodigal
[2023-06-29 05:05:06,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg509016b4-69b3-40d5-b7c6-22bbeced6341/GCA_015489145.1_ASM1548914v1_genomic.fna.gz | prodigal -d GCA_015489145.1_ASM1548914v1_genomic.fna/cds.fna -a GCA_015489145.1_ASM1548914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:05:16,172] [INFO] Task succeeded: Prodigal
[2023-06-29 05:05:16,173] [INFO] Task started: HMMsearch
[2023-06-29 05:05:16,173] [INFO] Running command: hmmsearch --tblout GCA_015489145.1_ASM1548914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference/reference_markers.hmm GCA_015489145.1_ASM1548914v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:05:16,447] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:05:16,448] [INFO] Found 6/6 markers.
[2023-06-29 05:05:16,494] [INFO] Query marker FASTA was written to GCA_015489145.1_ASM1548914v1_genomic.fna/markers.fasta
[2023-06-29 05:05:16,495] [INFO] Task started: Blastn
[2023-06-29 05:05:16,495] [INFO] Running command: blastn -query GCA_015489145.1_ASM1548914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference/reference_markers.fasta -out GCA_015489145.1_ASM1548914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:05:17,202] [INFO] Task succeeded: Blastn
[2023-06-29 05:05:17,207] [INFO] Selected 32 target genomes.
[2023-06-29 05:05:17,207] [INFO] Target genome list was writen to GCA_015489145.1_ASM1548914v1_genomic.fna/target_genomes.txt
[2023-06-29 05:05:17,217] [INFO] Task started: fastANI
[2023-06-29 05:05:17,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg509016b4-69b3-40d5-b7c6-22bbeced6341/GCA_015489145.1_ASM1548914v1_genomic.fna.gz --refList GCA_015489145.1_ASM1548914v1_genomic.fna/target_genomes.txt --output GCA_015489145.1_ASM1548914v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:05:46,440] [INFO] Task succeeded: fastANI
[2023-06-29 05:05:46,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:05:46,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:05:46,465] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:05:46,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 05:05:46,465] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2869	321	1124	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.252	352	1124	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	75.222	65	1124	95	below_threshold
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	75.1631	181	1124	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	75.1468	187	1124	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	75.142	183	1124	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.0744	204	1124	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	75.0648	175	1124	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	75.0596	175	1124	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.0472	210	1124	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	75.0445	146	1124	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.0427	202	1124	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.0102	249	1124	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	74.9993	112	1124	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.9885	250	1124	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9815	172	1124	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.9779	312	1124	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	74.977	63	1124	95	below_threshold
Nesterenkonia populi	strain=DSM 27959	GCA_007994735.1	1591087	1591087	type	True	74.9684	60	1124	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	74.9648	127	1124	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.9346	208	1124	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	74.9213	223	1124	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	74.8963	245	1124	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	74.854	281	1124	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	74.8471	309	1124	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	74.7906	300	1124	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	74.7897	298	1124	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	74.7723	272	1124	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 05:05:46,467] [INFO] DFAST Taxonomy check result was written to GCA_015489145.1_ASM1548914v1_genomic.fna/tc_result.tsv
[2023-06-29 05:05:46,468] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:05:46,468] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:05:46,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference/checkm_data
[2023-06-29 05:05:46,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:05:46,532] [INFO] Task started: CheckM
[2023-06-29 05:05:46,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015489145.1_ASM1548914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015489145.1_ASM1548914v1_genomic.fna/checkm_input GCA_015489145.1_ASM1548914v1_genomic.fna/checkm_result
[2023-06-29 05:06:20,210] [INFO] Task succeeded: CheckM
[2023-06-29 05:06:20,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 05:06:20,236] [INFO] ===== Completeness check finished =====
[2023-06-29 05:06:20,236] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:06:20,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015489145.1_ASM1548914v1_genomic.fna/markers.fasta)
[2023-06-29 05:06:20,237] [INFO] Task started: Blastn
[2023-06-29 05:06:20,237] [INFO] Running command: blastn -query GCA_015489145.1_ASM1548914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e94f1e6-3752-486e-b9d7-faa6780cea25/dqc_reference/reference_markers_gtdb.fasta -out GCA_015489145.1_ASM1548914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:06:21,272] [INFO] Task succeeded: Blastn
[2023-06-29 05:06:21,277] [INFO] Selected 22 target genomes.
[2023-06-29 05:06:21,277] [INFO] Target genome list was writen to GCA_015489145.1_ASM1548914v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:06:21,309] [INFO] Task started: fastANI
[2023-06-29 05:06:21,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg509016b4-69b3-40d5-b7c6-22bbeced6341/GCA_015489145.1_ASM1548914v1_genomic.fna.gz --refList GCA_015489145.1_ASM1548914v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015489145.1_ASM1548914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:06:40,697] [INFO] Task succeeded: fastANI
[2023-06-29 05:06:40,723] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 05:06:40,723] [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_015489145.1	s__S143-5 sp015489145	100.0	1107	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003694325.1	s__J125 sp003694325	77.2164	339	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__J125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845285.1	s__BH17 sp016845285	76.8836	213	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__BH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401435.1	s__M30B51 sp018401435	76.7786	351	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343455.1	s__UBA2385 sp002343455	76.4084	432	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152105.1	s__UBA2385 sp013152105	76.3506	196	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792625.1	s__JAEUKK01 sp016792625	76.236	497	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921785.1	s__SXON01 sp903921785	75.8929	360	1124	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_003695625.1	s__J065 sp003695625	75.3748	163	1124	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__J065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867695.1	s__VGIY01 sp016867695	75.1093	127	1124	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__CAIMUX01;f__WJJG01;g__VGIY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	75.0916	330	1124	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCF_008039875.1	s__Methylobacterium sp008039875	75.0804	209	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCA_017994815.1	s__JAGOJY01 sp017994815	75.0792	209	1124	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__JAGOJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201595.1	s__Sphaerotilus hippei	75.0495	179	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202835.1	s__Acidiphilium multivorum	75.0374	148	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	98.69	98.42	0.90	0.87	6	-
GCA_018241895.1	s__Rubrivivax sp018241895	75.031	168	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	75.0125	140	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503065.1	s__ALPHA2B sp005503065	74.9276	152	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	74.847	279	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935485.1	s__JAFGQW01 sp016935485	74.8157	148	1124	d__Bacteria;p__Planctomycetota;c__JAFGQW01;o__JAFGQW01;f__JAFGQW01;g__JAFGQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752025.1	s__Curtobacterium sp003752025	74.764	136	1124	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291955.1	s__UBA996 sp002291955	74.7297	85	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA996	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 05:06:40,725] [INFO] GTDB search result was written to GCA_015489145.1_ASM1548914v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:06:40,726] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:06:40,733] [INFO] DFAST_QC result json was written to GCA_015489145.1_ASM1548914v1_genomic.fna/dqc_result.json
[2023-06-29 05:06:40,733] [INFO] DFAST_QC completed!
[2023-06-29 05:06:40,733] [INFO] Total running time: 0h1m37s