[2024-01-24 12:45:10,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference
[2024-01-24 12:45:13,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,094] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,094] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2362369-b077-4f11-bd4b-cf94ed57def8/GCF_007644035.1_ASM764403v2_genomic.fna.gz | prodigal -d GCF_007644035.1_ASM764403v2_genomic.fna/cds.fna -a GCF_007644035.1_ASM764403v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:27,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:27,907] [INFO] Task started: HMMsearch
[2024-01-24 12:45:27,908] [INFO] Running command: hmmsearch --tblout GCF_007644035.1_ASM764403v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference/reference_markers.hmm GCF_007644035.1_ASM764403v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:28,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:28,210] [INFO] Found 6/6 markers.
[2024-01-24 12:45:28,251] [INFO] Query marker FASTA was written to GCF_007644035.1_ASM764403v2_genomic.fna/markers.fasta
[2024-01-24 12:45:28,252] [INFO] Task started: Blastn
[2024-01-24 12:45:28,252] [INFO] Running command: blastn -query GCF_007644035.1_ASM764403v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference/reference_markers.fasta -out GCF_007644035.1_ASM764403v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:29,136] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:29,139] [INFO] Selected 17 target genomes.
[2024-01-24 12:45:29,140] [INFO] Target genome list was writen to GCF_007644035.1_ASM764403v2_genomic.fna/target_genomes.txt
[2024-01-24 12:45:29,147] [INFO] Task started: fastANI
[2024-01-24 12:45:29,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2362369-b077-4f11-bd4b-cf94ed57def8/GCF_007644035.1_ASM764403v2_genomic.fna.gz --refList GCF_007644035.1_ASM764403v2_genomic.fna/target_genomes.txt --output GCF_007644035.1_ASM764403v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:43,475] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:43,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:43,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:43,495] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:43,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:43,495] [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
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	100.0	1244	1247	95	conclusive
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	87.189	1001	1247	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	82.1618	721	1247	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	82.1242	701	1247	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	82.0188	660	1247	95	below_threshold
Aquitalea aquatilis	strain=THG-DN7.12	GCA_005155025.1	1537400	1537400	type	True	79.7906	547	1247	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	79.6771	468	1247	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	79.602	505	1247	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	79.5239	490	1247	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	79.4705	496	1247	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	79.4219	473	1247	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	79.2981	501	1247	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	79.2922	550	1247	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	79.2485	497	1247	95	below_threshold
Chromobacterium haemolyticum	strain=DSM 19808	GCA_000711885.1	394935	394935	type	True	78.9154	466	1247	95	below_threshold
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	77.4821	233	1247	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	76.4365	99	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:43,497] [INFO] DFAST Taxonomy check result was written to GCF_007644035.1_ASM764403v2_genomic.fna/tc_result.tsv
[2024-01-24 12:45:43,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:43,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:43,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference/checkm_data
[2024-01-24 12:45:43,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:43,553] [INFO] Task started: CheckM
[2024-01-24 12:45:43,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007644035.1_ASM764403v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007644035.1_ASM764403v2_genomic.fna/checkm_input GCF_007644035.1_ASM764403v2_genomic.fna/checkm_result
[2024-01-24 12:46:28,804] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:28,807] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 22.72%
Strain heterogeneity: 7.69%
--------------------------------------------------------------------------------
[2024-01-24 12:46:28,839] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:28,840] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:28,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007644035.1_ASM764403v2_genomic.fna/markers.fasta)
[2024-01-24 12:46:28,840] [INFO] Task started: Blastn
[2024-01-24 12:46:28,840] [INFO] Running command: blastn -query GCF_007644035.1_ASM764403v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4d0322-6b88-47ff-b9fc-2612e4c4d317/dqc_reference/reference_markers_gtdb.fasta -out GCF_007644035.1_ASM764403v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:30,609] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:30,614] [INFO] Selected 11 target genomes.
[2024-01-24 12:46:30,614] [INFO] Target genome list was writen to GCF_007644035.1_ASM764403v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:30,631] [INFO] Task started: fastANI
[2024-01-24 12:46:30,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2362369-b077-4f11-bd4b-cf94ed57def8/GCF_007644035.1_ASM764403v2_genomic.fna.gz --refList GCF_007644035.1_ASM764403v2_genomic.fna/target_genomes_gtdb.txt --output GCF_007644035.1_ASM764403v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:40,173] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:40,183] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:46:40,184] [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_000335715.1	s__Vogesella sp000335715	91.0679	1044	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998615.1	s__Vogesella sp017998615	89.9689	684	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007644045.2	s__Vogesella urethralis	87.2017	1000	1247	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	82.7999	753	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	82.3726	683	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652475.1	s__Vogesella alkaliphila	82.1812	720	1247	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	82.1276	701	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	97.25	97.21	0.95	0.93	3	-
GCF_014652335.1	s__Vogesella fluminis	82.042	658	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325475.1	s__Chromobacterium phragmitis	79.5621	509	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_016428945.1	s__Chromobacterium sp016428945	79.4804	486	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_002081825.1	s__Chromobacterium haemolyticum_A	79.0205	490	1247	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.46	97.46	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:40,186] [INFO] GTDB search result was written to GCF_007644035.1_ASM764403v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:40,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:40,192] [INFO] DFAST_QC result json was written to GCF_007644035.1_ASM764403v2_genomic.fna/dqc_result.json
[2024-01-24 12:46:40,192] [INFO] DFAST_QC completed!
[2024-01-24 12:46:40,192] [INFO] Total running time: 0h1m30s