[2024-01-25 19:07:20,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:20,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:20,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference
[2024-01-25 19:07:21,648] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:21,649] [INFO] Task started: Prodigal
[2024-01-25 19:07:21,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c0f4a5e-ccc4-4261-ac9e-53e118a5c22b/GCF_003355495.1_ASM335549v1_genomic.fna.gz | prodigal -d GCF_003355495.1_ASM335549v1_genomic.fna/cds.fna -a GCF_003355495.1_ASM335549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:29,946] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:29,947] [INFO] Task started: HMMsearch
[2024-01-25 19:07:29,947] [INFO] Running command: hmmsearch --tblout GCF_003355495.1_ASM335549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference/reference_markers.hmm GCF_003355495.1_ASM335549v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:30,156] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:30,157] [INFO] Found 6/6 markers.
[2024-01-25 19:07:30,183] [INFO] Query marker FASTA was written to GCF_003355495.1_ASM335549v1_genomic.fna/markers.fasta
[2024-01-25 19:07:30,183] [INFO] Task started: Blastn
[2024-01-25 19:07:30,183] [INFO] Running command: blastn -query GCF_003355495.1_ASM335549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference/reference_markers.fasta -out GCF_003355495.1_ASM335549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:31,213] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:31,216] [INFO] Selected 15 target genomes.
[2024-01-25 19:07:31,216] [INFO] Target genome list was writen to GCF_003355495.1_ASM335549v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:31,242] [INFO] Task started: fastANI
[2024-01-25 19:07:31,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c0f4a5e-ccc4-4261-ac9e-53e118a5c22b/GCF_003355495.1_ASM335549v1_genomic.fna.gz --refList GCF_003355495.1_ASM335549v1_genomic.fna/target_genomes.txt --output GCF_003355495.1_ASM335549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:43,778] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:43,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:43,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:43,788] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:43,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:43,788] [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 cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	100.0	1084	1090	95	conclusive
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	88.5079	740	1090	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	81.6882	548	1090	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	81.668	532	1090	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	80.9272	543	1090	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	80.8896	551	1090	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	80.7735	547	1090	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	80.4908	513	1090	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	80.4088	471	1090	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	80.2581	498	1090	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.942	470	1090	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	79.7341	468	1090	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.4153	465	1090	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	78.6327	370	1090	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.4732	423	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:43,790] [INFO] DFAST Taxonomy check result was written to GCF_003355495.1_ASM335549v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:43,790] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:43,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:43,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference/checkm_data
[2024-01-25 19:07:43,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:43,825] [INFO] Task started: CheckM
[2024-01-25 19:07:43,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003355495.1_ASM335549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003355495.1_ASM335549v1_genomic.fna/checkm_input GCF_003355495.1_ASM335549v1_genomic.fna/checkm_result
[2024-01-25 19:08:11,716] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:11,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:11,744] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:11,744] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:11,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003355495.1_ASM335549v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:11,745] [INFO] Task started: Blastn
[2024-01-25 19:08:11,746] [INFO] Running command: blastn -query GCF_003355495.1_ASM335549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a30deb-3327-4ffa-b12e-04ff555466ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_003355495.1_ASM335549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:13,922] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:13,924] [INFO] Selected 14 target genomes.
[2024-01-25 19:08:13,924] [INFO] Target genome list was writen to GCF_003355495.1_ASM335549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:13,938] [INFO] Task started: fastANI
[2024-01-25 19:08:13,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c0f4a5e-ccc4-4261-ac9e-53e118a5c22b/GCF_003355495.1_ASM335549v1_genomic.fna.gz --refList GCF_003355495.1_ASM335549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003355495.1_ASM335549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:25,537] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:25,548] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:25,548] [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_003355495.1	s__Crenobacter cavernae	100.0	1083	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	conclusive
GCF_004345725.1	s__Crenobacter luteus	88.481	742	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_010435965.1	s__STGJ01 sp010435965	81.6967	547	1090	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	81.6686	532	1090	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	81.6385	633	1090	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	81.3766	591	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	81.05	600	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	81.0314	454	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652475.1	s__Vogesella alkaliphila	80.8817	552	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007705.1	s__Chromobacterium violaceum	80.8701	539	1090	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	80.6496	552	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855555.1	s__Chromobacterium sphagni	80.3601	471	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.33	99.33	0.93	0.93	2	-
GCF_008275125.1	s__Chromobacterium paludis	80.1241	483	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002213445.1	s__Chromobacterium sp002213445	80.0611	497	1090	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:08:25,551] [INFO] GTDB search result was written to GCF_003355495.1_ASM335549v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:25,552] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:25,556] [INFO] DFAST_QC result json was written to GCF_003355495.1_ASM335549v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:25,556] [INFO] DFAST_QC completed!
[2024-01-25 19:08:25,556] [INFO] Total running time: 0h1m5s