[2024-01-25 18:15:35,562] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference
[2024-01-25 18:15:36,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,722] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgb84a9bc1-280e-4c09-ad49-eb5b122e37d3/GCF_014042365.1_ASM1404236v1_genomic.fna.gz | prodigal -d GCF_014042365.1_ASM1404236v1_genomic.fna/cds.fna -a GCF_014042365.1_ASM1404236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:54,117] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:54,118] [INFO] Task started: HMMsearch
[2024-01-25 18:15:54,118] [INFO] Running command: hmmsearch --tblout GCF_014042365.1_ASM1404236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference/reference_markers.hmm GCF_014042365.1_ASM1404236v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:54,521] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:54,522] [INFO] Found 6/6 markers.
[2024-01-25 18:15:54,584] [INFO] Query marker FASTA was written to GCF_014042365.1_ASM1404236v1_genomic.fna/markers.fasta
[2024-01-25 18:15:54,584] [INFO] Task started: Blastn
[2024-01-25 18:15:54,584] [INFO] Running command: blastn -query GCF_014042365.1_ASM1404236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference/reference_markers.fasta -out GCF_014042365.1_ASM1404236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:55,605] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:55,608] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:55,608] [INFO] Target genome list was writen to GCF_014042365.1_ASM1404236v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:55,638] [INFO] Task started: fastANI
[2024-01-25 18:15:55,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgb84a9bc1-280e-4c09-ad49-eb5b122e37d3/GCF_014042365.1_ASM1404236v1_genomic.fna.gz --refList GCF_014042365.1_ASM1404236v1_genomic.fna/target_genomes.txt --output GCF_014042365.1_ASM1404236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:21,369] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:21,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:21,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:21,381] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:21,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:21,382] [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
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	100.0	1936	1938	95	conclusive
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	92.5996	1620	1938	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	91.2937	1560	1938	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	83.7683	1244	1938	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	83.7056	1218	1938	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	83.303	1158	1938	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	83.097	1112	1938	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	82.9904	1129	1938	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	82.9237	1055	1938	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	82.711	1128	1938	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	82.4195	995	1938	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	81.2749	1009	1938	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	81.2011	1025	1938	95	below_threshold
Massilia violaceinigra	strain=B2	GCA_002752675.1	2045208	2045208	type	True	81.0407	903	1938	95	below_threshold
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	80.5522	860	1938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:21,383] [INFO] DFAST Taxonomy check result was written to GCF_014042365.1_ASM1404236v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:21,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:21,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:21,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference/checkm_data
[2024-01-25 18:16:21,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:21,443] [INFO] Task started: CheckM
[2024-01-25 18:16:21,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014042365.1_ASM1404236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014042365.1_ASM1404236v1_genomic.fna/checkm_input GCF_014042365.1_ASM1404236v1_genomic.fna/checkm_result
[2024-01-25 18:17:14,779] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:14,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:14,799] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:14,799] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:14,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014042365.1_ASM1404236v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:14,800] [INFO] Task started: Blastn
[2024-01-25 18:17:14,800] [INFO] Running command: blastn -query GCF_014042365.1_ASM1404236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg550451c0-d8a0-483f-a1d4-d517807a43eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014042365.1_ASM1404236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:16,880] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:16,883] [INFO] Selected 13 target genomes.
[2024-01-25 18:17:16,883] [INFO] Target genome list was writen to GCF_014042365.1_ASM1404236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:16,899] [INFO] Task started: fastANI
[2024-01-25 18:17:16,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgb84a9bc1-280e-4c09-ad49-eb5b122e37d3/GCF_014042365.1_ASM1404236v1_genomic.fna.gz --refList GCF_014042365.1_ASM1404236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014042365.1_ASM1404236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:39,402] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:39,413] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:39,413] [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_014042365.1	s__LX47W sp014042365	100.0	1936	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014042345.1	s__LX47W sp014042345	92.6039	1618	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014042355.1	s__LX47W sp014042355	91.3038	1559	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LX47W	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416985.1	s__Duganella sp003416985	84.2562	1267	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	97.63	95.41	0.92	0.79	7	-
GCF_900114705.1	s__Rugamonas rubra	84.1096	1284	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCA_000381565.1	s__Duganella sp000381565	84.012	1290	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.03	95.03	0.82	0.82	2	-
GCF_013375995.1	s__Duganella sp013375995	83.9455	1231	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461825.1	s__Rugamonas sp016461825	83.8429	1272	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380215.1	s__Duganella sp009380215	83.75	1212	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000335815.1	s__Duganella sp000335815	83.7405	1252	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	95.81	95.66	0.89	0.89	4	-
GCF_013376005.1	s__Duganella sp013376005	83.3443	1138	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425045.1	s__Pseudoduganella sp001425045	83.2539	1184	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423125.1	s__Duganella sp001423125	82.8113	976	1938	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:39,417] [INFO] GTDB search result was written to GCF_014042365.1_ASM1404236v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:39,418] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:39,421] [INFO] DFAST_QC result json was written to GCF_014042365.1_ASM1404236v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:39,421] [INFO] DFAST_QC completed!
[2024-01-25 18:17:39,421] [INFO] Total running time: 0h2m4s