[2024-01-24 10:57:26,120] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,124] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference
[2024-01-24 10:57:27,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,578] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg7699a1a8-a7a6-4c5d-ae33-6d1282522b02/GCF_014652495.1_ASM1465249v1_genomic.fna.gz | prodigal -d GCF_014652495.1_ASM1465249v1_genomic.fna/cds.fna -a GCF_014652495.1_ASM1465249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:40,519] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:40,519] [INFO] Task started: HMMsearch
[2024-01-24 10:57:40,519] [INFO] Running command: hmmsearch --tblout GCF_014652495.1_ASM1465249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference/reference_markers.hmm GCF_014652495.1_ASM1465249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:40,786] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:40,788] [INFO] Found 6/6 markers.
[2024-01-24 10:57:40,821] [INFO] Query marker FASTA was written to GCF_014652495.1_ASM1465249v1_genomic.fna/markers.fasta
[2024-01-24 10:57:40,821] [INFO] Task started: Blastn
[2024-01-24 10:57:40,821] [INFO] Running command: blastn -query GCF_014652495.1_ASM1465249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference/reference_markers.fasta -out GCF_014652495.1_ASM1465249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:41,766] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:41,769] [INFO] Selected 20 target genomes.
[2024-01-24 10:57:41,769] [INFO] Target genome list was writen to GCF_014652495.1_ASM1465249v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:41,776] [INFO] Task started: fastANI
[2024-01-24 10:57:41,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg7699a1a8-a7a6-4c5d-ae33-6d1282522b02/GCF_014652495.1_ASM1465249v1_genomic.fna.gz --refList GCF_014652495.1_ASM1465249v1_genomic.fna/target_genomes.txt --output GCF_014652495.1_ASM1465249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:58,861] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:58,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:58,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:58,879] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:58,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:58,879] [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
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	100.0	1304	1307	95	conclusive
Paludibacterium paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	99.998	1307	1307	95	conclusive
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	79.3451	494	1307	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	79.2957	493	1307	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	79.2555	388	1307	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	79.24	457	1307	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.2016	429	1307	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	79.1976	491	1307	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	79.0642	340	1307	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.9955	442	1307	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.9808	470	1307	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.978	466	1307	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.9222	430	1307	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	78.908	455	1307	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	78.9076	349	1307	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	78.7479	473	1307	95	below_threshold
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	78.5287	334	1307	95	below_threshold
Aquitalea denitrificans	strain=5YN1-3	GCA_009856625.1	519081	519081	type	True	78.3563	322	1307	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	78.1503	315	1307	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.5566	183	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:58,881] [INFO] DFAST Taxonomy check result was written to GCF_014652495.1_ASM1465249v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:58,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:58,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:58,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference/checkm_data
[2024-01-24 10:57:58,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:58,926] [INFO] Task started: CheckM
[2024-01-24 10:57:58,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652495.1_ASM1465249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652495.1_ASM1465249v1_genomic.fna/checkm_input GCF_014652495.1_ASM1465249v1_genomic.fna/checkm_result
[2024-01-24 10:58:38,666] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:38,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:38,689] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:38,689] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:38,689] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652495.1_ASM1465249v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:38,690] [INFO] Task started: Blastn
[2024-01-24 10:58:38,690] [INFO] Running command: blastn -query GCF_014652495.1_ASM1465249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf8385b-6ac3-49d9-b8ce-57a4403a5104/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652495.1_ASM1465249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:40,277] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:40,280] [INFO] Selected 22 target genomes.
[2024-01-24 10:58:40,280] [INFO] Target genome list was writen to GCF_014652495.1_ASM1465249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:40,326] [INFO] Task started: fastANI
[2024-01-24 10:58:40,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg7699a1a8-a7a6-4c5d-ae33-6d1282522b02/GCF_014652495.1_ASM1465249v1_genomic.fna.gz --refList GCF_014652495.1_ASM1465249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652495.1_ASM1465249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:57,632] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:57,650] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:57,651] [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
GCF_018802605.1	s__Paludibacterium paludis	99.998	1307	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_018260425.1	s__Paludibacterium sp018260425	80.1708	585	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	79.4618	413	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007705.1	s__Chromobacterium violaceum	79.3668	493	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCA_002213445.1	s__Chromobacterium sp002213445	79.3111	458	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_001676875.1	s__Chromobacterium subtsugae	79.2631	473	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_000971335.1	s__Chromobacterium vaccinii	79.255	459	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_008275125.1	s__Chromobacterium paludis	79.2523	450	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	79.2458	390	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_003355495.1	s__Crenobacter cavernae	79.0603	339	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	79.0579	413	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000174355.1	s__Pseudogulbenkiania ferrooxidans_A	79.0299	422	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	78.9964	487	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_003052555.1	s__Chromobacterium sp003052555	78.9672	468	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325475.1	s__Chromobacterium phragmitis	78.9233	454	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_004363805.1	s__Paludibacterium purpuratum	78.9195	348	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232825.1	s__Paludibacterium sp019232825	78.8206	354	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.73	99.73	0.94	0.94	2	-
GCF_018802765.1	s__Paludibacterium sp018802765	78.7679	355	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855555.1	s__Chromobacterium sphagni	78.7478	473	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCF_000422925.1	s__Paludibacterium yongneupense	78.5044	336	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009856625.1	s__Aquitalea denitrificans	78.3324	324	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004346645.1	s__Gulbenkiania mobilis	78.2925	300	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Gulbenkiania	95.0	99.11	99.06	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:57,652] [INFO] GTDB search result was written to GCF_014652495.1_ASM1465249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:57,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:57,658] [INFO] DFAST_QC result json was written to GCF_014652495.1_ASM1465249v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:57,658] [INFO] DFAST_QC completed!
[2024-01-24 10:58:57,658] [INFO] Total running time: 0h1m32s