[2023-06-28 20:49:11,293] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:49:11,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:49:11,295] [INFO] DQC Reference Directory: /var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference
[2023-06-28 20:49:12,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:49:12,589] [INFO] Task started: Prodigal
[2023-06-28 20:49:12,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgc56ca6b4-f310-4080-a558-04a3f74edd5c/GCA_017998455.1_ASM1799845v1_genomic.fna.gz | prodigal -d GCA_017998455.1_ASM1799845v1_genomic.fna/cds.fna -a GCA_017998455.1_ASM1799845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:49:19,832] [INFO] Task succeeded: Prodigal
[2023-06-28 20:49:19,832] [INFO] Task started: HMMsearch
[2023-06-28 20:49:19,832] [INFO] Running command: hmmsearch --tblout GCA_017998455.1_ASM1799845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference/reference_markers.hmm GCA_017998455.1_ASM1799845v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:49:20,102] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:49:20,103] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc56ca6b4-f310-4080-a558-04a3f74edd5c/GCA_017998455.1_ASM1799845v1_genomic.fna.gz]
[2023-06-28 20:49:20,130] [INFO] Query marker FASTA was written to GCA_017998455.1_ASM1799845v1_genomic.fna/markers.fasta
[2023-06-28 20:49:20,130] [INFO] Task started: Blastn
[2023-06-28 20:49:20,130] [INFO] Running command: blastn -query GCA_017998455.1_ASM1799845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference/reference_markers.fasta -out GCA_017998455.1_ASM1799845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:49:20,873] [INFO] Task succeeded: Blastn
[2023-06-28 20:49:20,877] [INFO] Selected 15 target genomes.
[2023-06-28 20:49:20,877] [INFO] Target genome list was writen to GCA_017998455.1_ASM1799845v1_genomic.fna/target_genomes.txt
[2023-06-28 20:49:20,878] [INFO] Task started: fastANI
[2023-06-28 20:49:20,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgc56ca6b4-f310-4080-a558-04a3f74edd5c/GCA_017998455.1_ASM1799845v1_genomic.fna.gz --refList GCA_017998455.1_ASM1799845v1_genomic.fna/target_genomes.txt --output GCA_017998455.1_ASM1799845v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:49:31,639] [INFO] Task succeeded: fastANI
[2023-06-28 20:49:31,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:49:31,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:49:31,653] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:49:31,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:49:31,653] [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	78.8945	170	626	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	78.8047	187	626	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	78.7775	190	626	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.6376	188	626	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	78.6024	162	626	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.4538	156	626	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	78.238	174	626	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.065	130	626	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	78.0551	156	626	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	77.9798	139	626	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	77.9608	140	626	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.9367	168	626	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.8516	101	626	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	77.7226	111	626	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.5084	96	626	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:49:31,655] [INFO] DFAST Taxonomy check result was written to GCA_017998455.1_ASM1799845v1_genomic.fna/tc_result.tsv
[2023-06-28 20:49:31,656] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:49:31,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:49:31,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference/checkm_data
[2023-06-28 20:49:31,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:49:31,688] [INFO] Task started: CheckM
[2023-06-28 20:49:31,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017998455.1_ASM1799845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017998455.1_ASM1799845v1_genomic.fna/checkm_input GCA_017998455.1_ASM1799845v1_genomic.fna/checkm_result
[2023-06-28 20:49:59,411] [INFO] Task succeeded: CheckM
[2023-06-28 20:49:59,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:49:59,435] [INFO] ===== Completeness check finished =====
[2023-06-28 20:49:59,435] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:49:59,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017998455.1_ASM1799845v1_genomic.fna/markers.fasta)
[2023-06-28 20:49:59,436] [INFO] Task started: Blastn
[2023-06-28 20:49:59,436] [INFO] Running command: blastn -query GCA_017998455.1_ASM1799845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbef618d2-072d-45b8-a0a3-ff4a5ffa8309/dqc_reference/reference_markers_gtdb.fasta -out GCA_017998455.1_ASM1799845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:50:00,577] [INFO] Task succeeded: Blastn
[2023-06-28 20:50:00,582] [INFO] Selected 17 target genomes.
[2023-06-28 20:50:00,582] [INFO] Target genome list was writen to GCA_017998455.1_ASM1799845v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:50:00,589] [INFO] Task started: fastANI
[2023-06-28 20:50:00,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgc56ca6b4-f310-4080-a558-04a3f74edd5c/GCA_017998455.1_ASM1799845v1_genomic.fna.gz --refList GCA_017998455.1_ASM1799845v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017998455.1_ASM1799845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:50:11,903] [INFO] Task succeeded: fastANI
[2023-06-28 20:50:11,925] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:50:11,925] [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_011391115.1	s__JAABRC01 sp011391115	96.3682	288	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABRC01	95.0	97.47	97.41	0.69	0.69	3	conclusive
GCA_016703945.1	s__Rhodoferax sp016703945	79.5722	163	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795455.1	s__Rhodoferax sp001795455	78.7353	186	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCF_013334205.1	s__Hylemonella sp013334205	78.6617	163	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798165.1	s__Rhodoferax sp017798165	78.6415	181	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415675.1	s__Rhodoferax sp003415675	78.6151	189	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001432305.1	s__Hylemonella sp001432305	78.6136	159	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705575.1	s__Rhodoferax sp016705575	78.6075	155	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.15	99.12	0.95	0.95	5	-
GCA_002633085.1	s__Hylemonella sp002633085	78.4819	162	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	96.79	96.79	0.90	0.90	2	-
GCA_001797315.1	s__Hylemonella sp001797315	78.387	174	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_001592265.1	s__Hylemonella delicata	78.3852	176	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	78.323	161	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_018815325.1	s__Hylemonella sp018815325	78.2863	160	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.99	99.99	0.99	0.99	4	-
GCA_903897925.1	s__Rhodoferax sp903897925	78.264	122	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.65	99.65	0.87	0.87	2	-
GCA_002256115.1	s__Rhodoferax sp002256115	78.1699	139	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945325.1	s__Rhodoferax sp903945325	78.1177	156	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.68	99.56	0.89	0.88	4	-
GCA_001770955.1	s__Giesbergeria sp001770955	78.0527	140	626	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
--------------------------------------------------------------------------------
[2023-06-28 20:50:11,928] [INFO] GTDB search result was written to GCA_017998455.1_ASM1799845v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:50:11,929] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:50:11,933] [INFO] DFAST_QC result json was written to GCA_017998455.1_ASM1799845v1_genomic.fna/dqc_result.json
[2023-06-28 20:50:11,933] [INFO] DFAST_QC completed!
[2023-06-28 20:50:11,933] [INFO] Total running time: 0h1m1s