[2024-01-25 20:21:35,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference
[2024-01-25 20:21:36,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,682] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a422e01-f8e2-43b3-a2ea-7483bfc7d13e/GCF_000620105.1_ASM62010v1_genomic.fna.gz | prodigal -d GCF_000620105.1_ASM62010v1_genomic.fna/cds.fna -a GCF_000620105.1_ASM62010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:47,541] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:47,541] [INFO] Task started: HMMsearch
[2024-01-25 20:21:47,541] [INFO] Running command: hmmsearch --tblout GCF_000620105.1_ASM62010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference/reference_markers.hmm GCF_000620105.1_ASM62010v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:47,788] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:47,789] [INFO] Found 6/6 markers.
[2024-01-25 20:21:47,822] [INFO] Query marker FASTA was written to GCF_000620105.1_ASM62010v1_genomic.fna/markers.fasta
[2024-01-25 20:21:47,823] [INFO] Task started: Blastn
[2024-01-25 20:21:47,823] [INFO] Running command: blastn -query GCF_000620105.1_ASM62010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference/reference_markers.fasta -out GCF_000620105.1_ASM62010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:48,840] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:48,843] [INFO] Selected 22 target genomes.
[2024-01-25 20:21:48,843] [INFO] Target genome list was writen to GCF_000620105.1_ASM62010v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:48,868] [INFO] Task started: fastANI
[2024-01-25 20:21:48,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a422e01-f8e2-43b3-a2ea-7483bfc7d13e/GCF_000620105.1_ASM62010v1_genomic.fna.gz --refList GCF_000620105.1_ASM62010v1_genomic.fna/target_genomes.txt --output GCF_000620105.1_ASM62010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:05,573] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:05,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:05,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:05,587] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:22:05,587] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:22:05,587] [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 luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	79.4804	413	1315	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	79.4233	388	1315	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	79.3392	386	1315	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	79.2903	396	1315	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	79.1929	422	1315	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	79.053	445	1315	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	79.0397	439	1315	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	78.9862	433	1315	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	78.7949	408	1315	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.7904	377	1315	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	78.7798	383	1315	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.7201	408	1315	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	78.7133	402	1315	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.585	398	1315	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	78.5841	413	1315	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	78.5781	346	1315	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	78.5687	392	1315	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	78.1087	270	1315	95	below_threshold
Aquitalea pelogenes	strain=CCM 7557	GCA_001515305.1	1293573	1293573	type	True	77.9124	328	1315	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	77.5096	211	1315	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.6551	299	1315	95	below_threshold
Propionivibrio limicola	strain=GolChi1	GCA_009469695.1	167645	167645	type	True	76.5323	127	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:05,589] [INFO] DFAST Taxonomy check result was written to GCF_000620105.1_ASM62010v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:05,589] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:05,589] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:05,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference/checkm_data
[2024-01-25 20:22:05,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:05,631] [INFO] Task started: CheckM
[2024-01-25 20:22:05,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620105.1_ASM62010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620105.1_ASM62010v1_genomic.fna/checkm_input GCF_000620105.1_ASM62010v1_genomic.fna/checkm_result
[2024-01-25 20:22:44,623] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:44,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:44,643] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:44,643] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:44,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620105.1_ASM62010v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:44,644] [INFO] Task started: Blastn
[2024-01-25 20:22:44,644] [INFO] Running command: blastn -query GCF_000620105.1_ASM62010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eb9df92-f075-4cc3-9b00-6ca0a1502acb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620105.1_ASM62010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:46,534] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:46,537] [INFO] Selected 18 target genomes.
[2024-01-25 20:22:46,537] [INFO] Target genome list was writen to GCF_000620105.1_ASM62010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:46,566] [INFO] Task started: fastANI
[2024-01-25 20:22:46,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a422e01-f8e2-43b3-a2ea-7483bfc7d13e/GCF_000620105.1_ASM62010v1_genomic.fna.gz --refList GCF_000620105.1_ASM62010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620105.1_ASM62010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:59,992] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:00,004] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:00,004] [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_000620105.1	s__Microvirgula aerodenitrificans	100.0	1310	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Microvirgula	95.0	99.13	99.12	0.93	0.93	3	conclusive
GCF_000423285.1	s__Laribacter hongkongensis	79.7738	481	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	98.14	97.82	0.92	0.90	5	-
GCF_004345725.1	s__Crenobacter luteus	79.4992	411	1315	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	79.3392	386	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055005.1	s__Laribacter sp018055005	79.3341	391	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	99.59	99.59	0.84	0.84	2	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	79.2206	435	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633895.1	s__Vogesella indigofera	79.1929	422	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	79.0282	423	1315	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	79.0022	443	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	78.9671	323	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002848345.1	s__Chromobacterium sp002848345	78.8535	461	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	78.7919	426	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
GCF_008275125.1	s__Chromobacterium paludis	78.785	381	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	78.7284	419	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016937655.1	s__Chromobacterium alkanivorans	78.5551	433	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
GCF_003201855.1	s__Rivicola pingtungensis	78.549	348	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002905.1	s__Rivicola sp002002905	78.2444	335	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192435.1	s__Sulfuritalea sp016192435	76.5377	172	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:00,005] [INFO] GTDB search result was written to GCF_000620105.1_ASM62010v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:00,006] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:00,009] [INFO] DFAST_QC result json was written to GCF_000620105.1_ASM62010v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:00,009] [INFO] DFAST_QC completed!
[2024-01-25 20:23:00,010] [INFO] Total running time: 0h1m24s