[2024-01-24 14:07:30,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:30,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:30,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference
[2024-01-24 14:07:31,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:31,841] [INFO] Task started: Prodigal
[2024-01-24 14:07:31,842] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d404422-6dec-4b5f-bd40-82a6c7263bff/GCF_001855565.1_ASM185556v1_genomic.fna.gz | prodigal -d GCF_001855565.1_ASM185556v1_genomic.fna/cds.fna -a GCF_001855565.1_ASM185556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:44,809] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:44,810] [INFO] Task started: HMMsearch
[2024-01-24 14:07:44,810] [INFO] Running command: hmmsearch --tblout GCF_001855565.1_ASM185556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference/reference_markers.hmm GCF_001855565.1_ASM185556v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:45,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:45,115] [INFO] Found 6/6 markers.
[2024-01-24 14:07:45,154] [INFO] Query marker FASTA was written to GCF_001855565.1_ASM185556v1_genomic.fna/markers.fasta
[2024-01-24 14:07:45,155] [INFO] Task started: Blastn
[2024-01-24 14:07:45,155] [INFO] Running command: blastn -query GCF_001855565.1_ASM185556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference/reference_markers.fasta -out GCF_001855565.1_ASM185556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:46,204] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:46,208] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:46,208] [INFO] Target genome list was writen to GCF_001855565.1_ASM185556v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:46,213] [INFO] Task started: fastANI
[2024-01-24 14:07:46,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d404422-6dec-4b5f-bd40-82a6c7263bff/GCF_001855565.1_ASM185556v1_genomic.fna.gz --refList GCF_001855565.1_ASM185556v1_genomic.fna/target_genomes.txt --output GCF_001855565.1_ASM185556v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:58,916] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:58,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:58,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:58,930] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:58,930] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:07:58,930] [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
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	100.0	1314	1319	95	inconclusive
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	95.0184	1146	1319	95	inconclusive
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	87.6765	1031	1319	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	87.5769	1050	1319	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	87.5227	1055	1319	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	87.2417	1009	1319	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	86.9373	1022	1319	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	86.7241	1000	1319	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	86.6347	1023	1319	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	83.0235	835	1319	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	77.5958	102	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:58,932] [INFO] DFAST Taxonomy check result was written to GCF_001855565.1_ASM185556v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:58,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:58,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:58,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference/checkm_data
[2024-01-24 14:07:58,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:58,974] [INFO] Task started: CheckM
[2024-01-24 14:07:58,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001855565.1_ASM185556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001855565.1_ASM185556v1_genomic.fna/checkm_input GCF_001855565.1_ASM185556v1_genomic.fna/checkm_result
[2024-01-24 14:08:39,689] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:39,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:39,717] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:39,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:39,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001855565.1_ASM185556v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:39,719] [INFO] Task started: Blastn
[2024-01-24 14:08:39,719] [INFO] Running command: blastn -query GCF_001855565.1_ASM185556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea7dfd8d-1ef7-40c0-b4d7-963f284c76f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001855565.1_ASM185556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:41,878] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:41,882] [INFO] Selected 8 target genomes.
[2024-01-24 14:08:41,882] [INFO] Target genome list was writen to GCF_001855565.1_ASM185556v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:41,888] [INFO] Task started: fastANI
[2024-01-24 14:08:41,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d404422-6dec-4b5f-bd40-82a6c7263bff/GCF_001855565.1_ASM185556v1_genomic.fna.gz --refList GCF_001855565.1_ASM185556v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001855565.1_ASM185556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:52,082] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:52,098] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:52,099] [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_001855565.1	s__Chromobacterium amazonense	100.0	1313	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	conclusive
GCF_016428945.1	s__Chromobacterium sp016428945	94.9044	1133	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_008275125.1	s__Chromobacterium paludis	87.6765	1031	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007705.1	s__Chromobacterium violaceum	87.5351	1053	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_002924365.1	s__Chromobacterium sp002924365	87.248	1008	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971335.1	s__Chromobacterium vaccinii	86.9668	1019	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	86.8336	1024	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_003325475.1	s__Chromobacterium phragmitis	86.6211	1022	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:52,100] [INFO] GTDB search result was written to GCF_001855565.1_ASM185556v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:52,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:52,105] [INFO] DFAST_QC result json was written to GCF_001855565.1_ASM185556v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:52,105] [INFO] DFAST_QC completed!
[2024-01-24 14:08:52,105] [INFO] Total running time: 0h1m22s