[2024-01-24 13:58:10,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference
[2024-01-24 13:58:12,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,009] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8d48cbd-b376-482e-836f-e413fcd773b3/GCF_009831765.1_ASM983176v1_genomic.fna.gz | prodigal -d GCF_009831765.1_ASM983176v1_genomic.fna/cds.fna -a GCF_009831765.1_ASM983176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:23,045] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:23,045] [INFO] Task started: HMMsearch
[2024-01-24 13:58:23,046] [INFO] Running command: hmmsearch --tblout GCF_009831765.1_ASM983176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference/reference_markers.hmm GCF_009831765.1_ASM983176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:23,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:23,308] [INFO] Found 6/6 markers.
[2024-01-24 13:58:23,340] [INFO] Query marker FASTA was written to GCF_009831765.1_ASM983176v1_genomic.fna/markers.fasta
[2024-01-24 13:58:23,341] [INFO] Task started: Blastn
[2024-01-24 13:58:23,341] [INFO] Running command: blastn -query GCF_009831765.1_ASM983176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference/reference_markers.fasta -out GCF_009831765.1_ASM983176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,334] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,338] [INFO] Selected 23 target genomes.
[2024-01-24 13:58:24,339] [INFO] Target genome list was writen to GCF_009831765.1_ASM983176v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,401] [INFO] Task started: fastANI
[2024-01-24 13:58:24,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d48cbd-b376-482e-836f-e413fcd773b3/GCF_009831765.1_ASM983176v1_genomic.fna.gz --refList GCF_009831765.1_ASM983176v1_genomic.fna/target_genomes.txt --output GCF_009831765.1_ASM983176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:40,680] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:40,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:40,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:40,698] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:40,699] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:40,699] [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
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	80.4656	543	1054	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	80.3199	539	1054	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	79.1506	364	1054	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	79.047	387	1054	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	78.9782	376	1054	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	78.8307	344	1054	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.8188	342	1054	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	78.7766	359	1054	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	78.745	396	1054	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.716	372	1054	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	78.6007	371	1054	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.6004	288	1054	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	78.5992	376	1054	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.569	355	1054	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	78.3406	276	1054	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	77.9806	235	1054	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	77.8504	247	1054	95	below_threshold
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	77.7047	231	1054	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.9672	212	1054	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	76.1181	90	1054	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	76.1181	90	1054	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	75.9969	50	1054	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	75.9841	120	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:40,704] [INFO] DFAST Taxonomy check result was written to GCF_009831765.1_ASM983176v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:40,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:40,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:40,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference/checkm_data
[2024-01-24 13:58:40,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:40,743] [INFO] Task started: CheckM
[2024-01-24 13:58:40,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009831765.1_ASM983176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009831765.1_ASM983176v1_genomic.fna/checkm_input GCF_009831765.1_ASM983176v1_genomic.fna/checkm_result
[2024-01-24 13:59:15,294] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:15,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:15,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:15,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:15,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009831765.1_ASM983176v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:15,319] [INFO] Task started: Blastn
[2024-01-24 13:59:15,319] [INFO] Running command: blastn -query GCF_009831765.1_ASM983176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1f7c619-1a10-4a5b-8770-54523eec3c99/dqc_reference/reference_markers_gtdb.fasta -out GCF_009831765.1_ASM983176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:16,916] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:16,921] [INFO] Selected 20 target genomes.
[2024-01-24 13:59:16,921] [INFO] Target genome list was writen to GCF_009831765.1_ASM983176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:17,016] [INFO] Task started: fastANI
[2024-01-24 13:59:17,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d48cbd-b376-482e-836f-e413fcd773b3/GCF_009831765.1_ASM983176v1_genomic.fna.gz --refList GCF_009831765.1_ASM983176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009831765.1_ASM983176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:30,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:30,711] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:30,711] [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_003856275.1	s__STGJ01 sp003856275	97.9116	951	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	97.91	97.91	0.91	0.91	2	conclusive
GCF_010435965.1	s__STGJ01 sp010435965	80.4673	543	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919095.1	s__STGJ01 sp004919095	80.2989	541	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652335.1	s__Vogesella fluminis	79.1512	364	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633895.1	s__Vogesella indigofera	79.0409	388	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_014652475.1	s__Vogesella alkaliphila	78.9934	375	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	78.8882	337	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428945.1	s__Chromobacterium sp016428945	78.7678	360	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_000174355.1	s__Pseudogulbenkiania ferrooxidans_A	78.7476	340	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCF_902829295.1	s__Vogesella oryzae	78.7189	357	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	78.7184	383	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	78.7078	389	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	78.6151	287	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_000007705.1	s__Chromobacterium violaceum	78.5958	370	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_002848345.1	s__Chromobacterium sp002848345	78.505	355	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	78.4197	268	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	78.3402	276	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCA_009707705.1	s__WLYX01 sp009707705	78.0913	266	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__WLYX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422925.1	s__Paludibacterium yongneupense	77.7047	231	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014860395.1	s__2-12-FULL-64-23 sp014860395	75.8062	68	1054	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-39;g__2-12-FULL-64-23	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:30,713] [INFO] GTDB search result was written to GCF_009831765.1_ASM983176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:30,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:30,719] [INFO] DFAST_QC result json was written to GCF_009831765.1_ASM983176v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:30,719] [INFO] DFAST_QC completed!
[2024-01-24 13:59:30,719] [INFO] Total running time: 0h1m20s