[2024-01-24 13:28:11,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference
[2024-01-24 13:28:12,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:12,970] [INFO] Task started: Prodigal
[2024-01-24 13:28:12,970] [INFO] Running command: gunzip -c /var/lib/cwl/stga6ba6c4f-6146-499b-a47f-47b236ccf8f3/GCF_000423285.1_ASM42328v1_genomic.fna.gz | prodigal -d GCF_000423285.1_ASM42328v1_genomic.fna/cds.fna -a GCF_000423285.1_ASM42328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:22,914] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:22,914] [INFO] Task started: HMMsearch
[2024-01-24 13:28:22,915] [INFO] Running command: hmmsearch --tblout GCF_000423285.1_ASM42328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference/reference_markers.hmm GCF_000423285.1_ASM42328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:23,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:23,173] [INFO] Found 6/6 markers.
[2024-01-24 13:28:23,214] [INFO] Query marker FASTA was written to GCF_000423285.1_ASM42328v1_genomic.fna/markers.fasta
[2024-01-24 13:28:23,214] [INFO] Task started: Blastn
[2024-01-24 13:28:23,215] [INFO] Running command: blastn -query GCF_000423285.1_ASM42328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference/reference_markers.fasta -out GCF_000423285.1_ASM42328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:24,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:24,170] [INFO] Selected 25 target genomes.
[2024-01-24 13:28:24,170] [INFO] Target genome list was writen to GCF_000423285.1_ASM42328v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:24,285] [INFO] Task started: fastANI
[2024-01-24 13:28:24,285] [INFO] Running command: fastANI --query /var/lib/cwl/stga6ba6c4f-6146-499b-a47f-47b236ccf8f3/GCF_000423285.1_ASM42328v1_genomic.fna.gz --refList GCF_000423285.1_ASM42328v1_genomic.fna/target_genomes.txt --output GCF_000423285.1_ASM42328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:41,412] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:41,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:41,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:41,431] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:41,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:41,432] [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 intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	79.1065	343	1018	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	79.0129	351	1018	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.782	329	1018	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	78.6316	317	1018	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	78.5929	300	1018	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	78.5488	306	1018	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	78.5065	299	1018	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	78.4673	317	1018	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	78.4661	334	1018	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.4346	299	1018	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.4231	306	1018	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	78.3419	319	1018	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.2968	313	1018	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.2946	313	1018	95	below_threshold
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	77.9916	223	1018	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	77.465	142	1018	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	77.4568	144	1018	95	below_threshold
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	77.2078	178	1018	95	below_threshold
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	77.1251	148	1018	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	76.9173	190	1018	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	76.6698	132	1018	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	76.6301	132	1018	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	76.4819	192	1018	95	below_threshold
Caballeronia glathei	strain=DSM 50014	GCA_000698595.1	60547	60547	type	True	76.1867	119	1018	95	below_threshold
Caballeronia glathei	strain=LMG 14190	GCA_000751215.2	60547	60547	type	True	76.1639	116	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,433] [INFO] DFAST Taxonomy check result was written to GCF_000423285.1_ASM42328v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:41,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:41,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:41,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference/checkm_data
[2024-01-24 13:28:41,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:41,465] [INFO] Task started: CheckM
[2024-01-24 13:28:41,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423285.1_ASM42328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423285.1_ASM42328v1_genomic.fna/checkm_input GCF_000423285.1_ASM42328v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,364] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,387] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423285.1_ASM42328v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,389] [INFO] Task started: Blastn
[2024-01-24 13:29:15,389] [INFO] Running command: blastn -query GCF_000423285.1_ASM42328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69191145-01a3-4546-892a-5f0fa296aadf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423285.1_ASM42328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:17,145] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:17,150] [INFO] Selected 20 target genomes.
[2024-01-24 13:29:17,151] [INFO] Target genome list was writen to GCF_000423285.1_ASM42328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:17,360] [INFO] Task started: fastANI
[2024-01-24 13:29:17,360] [INFO] Running command: fastANI --query /var/lib/cwl/stga6ba6c4f-6146-499b-a47f-47b236ccf8f3/GCF_000423285.1_ASM42328v1_genomic.fna.gz --refList GCF_000423285.1_ASM42328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423285.1_ASM42328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:31,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:31,391] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:31,392] [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_000423285.1	s__Laribacter hongkongensis	100.0	1014	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	98.14	97.82	0.92	0.90	5	conclusive
GCA_018055005.1	s__Laribacter sp018055005	93.8491	699	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	99.59	99.59	0.84	0.84	2	-
GCF_000620105.1	s__Microvirgula aerodenitrificans	79.9511	479	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Microvirgula	95.0	99.13	99.12	0.93	0.93	3	-
GCF_004919095.1	s__STGJ01 sp004919095	79.0929	344	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010435965.1	s__STGJ01 sp010435965	79.0261	350	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	78.9976	330	1018	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	78.8498	337	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCA_002213445.1	s__Chromobacterium sp002213445	78.8493	320	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_003633895.1	s__Vogesella indigofera	78.6533	357	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_003201855.1	s__Rivicola pingtungensis	78.651	315	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	78.6148	336	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855555.1	s__Chromobacterium sphagni	78.557	307	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCF_001855565.1	s__Chromobacterium amazonense	78.422	301	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_016428945.1	s__Chromobacterium sp016428945	78.3985	311	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_002002905.1	s__Rivicola sp002002905	78.3423	308	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937655.1	s__Chromobacterium alkanivorans	78.3417	319	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
GCA_013335435.1	s__Parasulfuritortus sp013335435	77.0555	151	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Parasulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234655.1	s__Sulfuritortus sp016234655	76.8973	142	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:31,393] [INFO] GTDB search result was written to GCF_000423285.1_ASM42328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:31,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:31,398] [INFO] DFAST_QC result json was written to GCF_000423285.1_ASM42328v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:31,398] [INFO] DFAST_QC completed!
[2024-01-24 13:29:31,399] [INFO] Total running time: 0h1m20s