[2023-06-29 21:20:38,790] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:20:38,792] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:20:38,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference
[2023-06-29 21:20:40,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:20:40,174] [INFO] Task started: Prodigal
[2023-06-29 21:20:40,174] [INFO] Running command: gunzip -c /var/lib/cwl/stg37b4f63c-f59f-4e75-969e-385e3f39f04f/GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna.gz | prodigal -d GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/cds.fna -a GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:20:51,601] [INFO] Task succeeded: Prodigal
[2023-06-29 21:20:51,602] [INFO] Task started: HMMsearch
[2023-06-29 21:20:51,602] [INFO] Running command: hmmsearch --tblout GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference/reference_markers.hmm GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:20:51,905] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:20:51,906] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg37b4f63c-f59f-4e75-969e-385e3f39f04f/GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna.gz]
[2023-06-29 21:20:51,957] [INFO] Query marker FASTA was written to GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/markers.fasta
[2023-06-29 21:20:51,958] [INFO] Task started: Blastn
[2023-06-29 21:20:51,958] [INFO] Running command: blastn -query GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/markers.fasta -db /var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference/reference_markers.fasta -out GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:20:52,686] [INFO] Task succeeded: Blastn
[2023-06-29 21:20:52,690] [INFO] Selected 16 target genomes.
[2023-06-29 21:20:52,691] [INFO] Target genome list was writen to GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/target_genomes.txt
[2023-06-29 21:20:52,692] [INFO] Task started: fastANI
[2023-06-29 21:20:52,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg37b4f63c-f59f-4e75-969e-385e3f39f04f/GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna.gz --refList GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/target_genomes.txt --output GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:21:03,938] [INFO] Task succeeded: fastANI
[2023-06-29 21:21:03,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:21:03,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:21:03,956] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:21:03,957] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:21:03,957] [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
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	79.3498	263	651	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	79.3227	263	651	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	78.9787	229	651	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	78.9641	231	651	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.282	215	651	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.8826	197	651	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.7522	148	651	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	77.4241	143	651	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.3006	159	651	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.1955	143	651	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	77.1927	131	651	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	77.0798	137	651	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.6271	90	651	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.6222	86	651	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	76.6061	94	651	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	76.3005	86	651	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:21:03,960] [INFO] DFAST Taxonomy check result was written to GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/tc_result.tsv
[2023-06-29 21:21:03,960] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:21:03,961] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:21:03,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference/checkm_data
[2023-06-29 21:21:03,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:21:04,005] [INFO] Task started: CheckM
[2023-06-29 21:21:04,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/checkm_input GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/checkm_result
[2023-06-29 21:21:42,087] [INFO] Task succeeded: CheckM
[2023-06-29 21:21:42,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.24%
Contamintation: 9.61%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-29 21:21:42,114] [INFO] ===== Completeness check finished =====
[2023-06-29 21:21:42,115] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:21:42,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/markers.fasta)
[2023-06-29 21:21:42,116] [INFO] Task started: Blastn
[2023-06-29 21:21:42,116] [INFO] Running command: blastn -query GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/markers.fasta -db /var/lib/cwl/stg634333f3-2097-4d5a-b8c7-34c2194b5c3b/dqc_reference/reference_markers_gtdb.fasta -out GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:21:43,361] [INFO] Task succeeded: Blastn
[2023-06-29 21:21:43,366] [INFO] Selected 21 target genomes.
[2023-06-29 21:21:43,366] [INFO] Target genome list was writen to GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:21:43,377] [INFO] Task started: fastANI
[2023-06-29 21:21:43,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg37b4f63c-f59f-4e75-969e-385e3f39f04f/GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna.gz --refList GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/target_genomes_gtdb.txt --output GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:21:57,314] [INFO] Task succeeded: fastANI
[2023-06-29 21:21:57,342] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:21:57,342] [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_903886165.1	s__Rhodoferax sp903886165	79.7424	208	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.81	98.69	0.69	0.69	3	-
GCA_002842265.1	s__Rhodoferax sp002842265	79.536	251	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001771065.1	s__Rhodoferax sp001771065	79.5208	272	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391645.1	s__Rhodoferax sp011391645	79.4622	259	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001871515.1	s__Rhodoferax sp001871515	79.3814	236	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.47	99.26	0.89	0.81	6	-
GCA_008080595.1	s__Rhodoferax sp008080595	79.3432	331	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002017865.1	s__Rhodoferax fermentans	79.3043	264	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002083775.1	s__Rhodoferax ferrireducens_A	79.2219	293	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619435.1	s__Rhodoferax sp018619435	79.1052	266	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416775.1	s__Rhodoferax sp013416775	79.0758	262	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719055.1	s__Rhodoferax sp016719055	79.0202	280	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905735.1	s__Rhodoferax sp903905735	79.0135	275	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938565.1	s__Rhodoferax antarcticus	79.0119	228	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.95	0.95	2	-
GCA_002789915.1	s__Rhodoferax sp002789915	78.8808	236	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.63	99.52	0.89	0.89	3	-
GCA_002786915.1	s__Rhodoferax sp002786915	78.4378	231	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002381045.1	s__Rhodoferax sp002381045	78.3302	213	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	96.07	96.07	0.76	0.76	2	-
GCA_903960915.1	s__Rhodoferax sp903960915	78.1923	188	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_018061265.1	s__Rhodoferax sp018061265	78.0563	226	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.89	0.89	2	-
GCA_001795455.1	s__Rhodoferax sp001795455	77.6194	178	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCA_903870955.1	s__Rhodoferax sp903870955	77.4242	99	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.51	98.51	0.73	0.73	2	-
GCA_013297935.1	s__Rhodoferax sp013297935	77.3747	143	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 21:21:57,344] [INFO] GTDB search result was written to GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/result_gtdb.tsv
[2023-06-29 21:21:57,345] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:21:57,349] [INFO] DFAST_QC result json was written to GCA_903916635.1_freshwater_MAG_---_Loclat_bin-18675_genomic.fna/dqc_result.json
[2023-06-29 21:21:57,349] [INFO] DFAST_QC completed!
[2023-06-29 21:21:57,349] [INFO] Total running time: 0h1m19s