[2023-06-30 20:26:36,339] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:26:36,343] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:26:36,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference
[2023-06-30 20:26:37,697] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:26:37,698] [INFO] Task started: Prodigal
[2023-06-30 20:26:37,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg40935cef-ddee-4ece-9927-93246d46fe08/GCA_016708345.1_ASM1670834v1_genomic.fna.gz | prodigal -d GCA_016708345.1_ASM1670834v1_genomic.fna/cds.fna -a GCA_016708345.1_ASM1670834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:26:55,725] [INFO] Task succeeded: Prodigal
[2023-06-30 20:26:55,725] [INFO] Task started: HMMsearch
[2023-06-30 20:26:55,725] [INFO] Running command: hmmsearch --tblout GCA_016708345.1_ASM1670834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference/reference_markers.hmm GCA_016708345.1_ASM1670834v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:26:56,036] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:26:56,037] [INFO] Found 6/6 markers.
[2023-06-30 20:26:56,079] [INFO] Query marker FASTA was written to GCA_016708345.1_ASM1670834v1_genomic.fna/markers.fasta
[2023-06-30 20:26:56,079] [INFO] Task started: Blastn
[2023-06-30 20:26:56,079] [INFO] Running command: blastn -query GCA_016708345.1_ASM1670834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference/reference_markers.fasta -out GCA_016708345.1_ASM1670834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:26:56,893] [INFO] Task succeeded: Blastn
[2023-06-30 20:26:56,898] [INFO] Selected 23 target genomes.
[2023-06-30 20:26:56,898] [INFO] Target genome list was writen to GCA_016708345.1_ASM1670834v1_genomic.fna/target_genomes.txt
[2023-06-30 20:26:56,899] [INFO] Task started: fastANI
[2023-06-30 20:26:56,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg40935cef-ddee-4ece-9927-93246d46fe08/GCA_016708345.1_ASM1670834v1_genomic.fna.gz --refList GCA_016708345.1_ASM1670834v1_genomic.fna/target_genomes.txt --output GCA_016708345.1_ASM1670834v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:27:14,908] [INFO] Task succeeded: fastANI
[2023-06-30 20:27:14,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:27:14,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:27:14,933] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:27:14,933] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:27:14,933] [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 ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	79.2031	486	1630	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.934	411	1630	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	78.768	401	1630	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	78.711	400	1630	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	78.5577	387	1630	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	78.5185	387	1630	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	78.3949	363	1630	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	78.2018	402	1630	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	78.2007	353	1630	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	78.1936	387	1630	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	78.0693	290	1630	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	78.0543	295	1630	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.0535	344	1630	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	78.0521	338	1630	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	77.6997	296	1630	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	77.605	291	1630	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	77.5625	264	1630	95	below_threshold
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	77.539	212	1630	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	77.3989	203	1630	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	77.3857	222	1630	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	77.1334	233	1630	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	77.0291	199	1630	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:27:14,935] [INFO] DFAST Taxonomy check result was written to GCA_016708345.1_ASM1670834v1_genomic.fna/tc_result.tsv
[2023-06-30 20:27:14,936] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:27:14,936] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:27:14,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference/checkm_data
[2023-06-30 20:27:14,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:27:14,984] [INFO] Task started: CheckM
[2023-06-30 20:27:14,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708345.1_ASM1670834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708345.1_ASM1670834v1_genomic.fna/checkm_input GCA_016708345.1_ASM1670834v1_genomic.fna/checkm_result
[2023-06-30 20:28:09,507] [INFO] Task succeeded: CheckM
[2023-06-30 20:28:09,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:28:09,532] [INFO] ===== Completeness check finished =====
[2023-06-30 20:28:09,533] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:28:09,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708345.1_ASM1670834v1_genomic.fna/markers.fasta)
[2023-06-30 20:28:09,533] [INFO] Task started: Blastn
[2023-06-30 20:28:09,534] [INFO] Running command: blastn -query GCA_016708345.1_ASM1670834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c965a3f-d087-4305-a1ad-5b0dd1e18853/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708345.1_ASM1670834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:28:10,873] [INFO] Task succeeded: Blastn
[2023-06-30 20:28:10,878] [INFO] Selected 21 target genomes.
[2023-06-30 20:28:10,879] [INFO] Target genome list was writen to GCA_016708345.1_ASM1670834v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:28:10,881] [INFO] Task started: fastANI
[2023-06-30 20:28:10,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg40935cef-ddee-4ece-9927-93246d46fe08/GCA_016708345.1_ASM1670834v1_genomic.fna.gz --refList GCA_016708345.1_ASM1670834v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708345.1_ASM1670834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:28:27,596] [INFO] Task succeeded: fastANI
[2023-06-30 20:28:27,617] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:28:27,618] [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_016708345.1	s__Rhodoferax sp016708345	100.0	1626	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.29	99.29	0.95	0.95	2	conclusive
GCA_016719405.1	s__Rhodoferax sp016719405	80.3503	521	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	98.38	98.38	0.86	0.86	2	-
GCA_002413825.1	s__Rhodoferax sp002413825	79.6402	510	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347515.1	s__Rhodoferax sp003347515	79.5174	568	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780565.1	s__Rhodoferax sp018780565	79.4623	476	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770935.1	s__Rhodoferax sp001770935	79.4403	486	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422455.1	s__Rhodoferax sp002422455	79.3038	266	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013605.1	s__Rhodoferax ferrireducens	79.2124	484	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	95.18	95.18	0.88	0.88	2	-
GCF_003415675.1	s__Rhodoferax sp003415675	78.92	414	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791765.1	s__Rhodoferax sp013791765	78.9022	450	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.97	99.92	0.98	0.96	7	-
GCA_010365055.1	s__Rhodoferax sp010365055	78.8913	448	1630	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	78.556	390	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903823025.1	s__Rhodoferax sp903823025	78.3369	368	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.95	99.83	0.97	0.95	6	-
GCF_002002705.1	s__Rhodoferax_A sp002002705	78.2994	341	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938565.1	s__Rhodoferax antarcticus	78.2292	382	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.95	0.95	2	-
GCA_017997975.1	s__Rhodoferax sp017997975	78.1999	281	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104385.1	s__Rhodoferax_B sp900104385	78.1129	352	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185015.1	s__Hylemonella sp016185015	77.8952	330	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517545.1	s__Limnohabitans_A sp001517545	77.892	274	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.89	95.29	0.97	0.96	4	-
GCA_903876045.1	s__Rhodoferax sp903876045	77.5518	262	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.28	99.14	0.84	0.81	3	-
GCF_014637085.1	s__Comamonas phosphati	77.5512	265	1630	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:28:27,620] [INFO] GTDB search result was written to GCA_016708345.1_ASM1670834v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:28:27,621] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:28:27,625] [INFO] DFAST_QC result json was written to GCA_016708345.1_ASM1670834v1_genomic.fna/dqc_result.json
[2023-06-30 20:28:27,626] [INFO] DFAST_QC completed!
[2023-06-30 20:28:27,626] [INFO] Total running time: 0h1m51s