[2024-01-24 14:19:46,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,156] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference
[2024-01-24 14:19:47,470] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,471] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,471] [INFO] Running command: gunzip -c /var/lib/cwl/stg368f677a-5b62-44e2-a73e-7f0bb2ac1f5f/GCF_004341885.1_ASM434188v1_genomic.fna.gz | prodigal -d GCF_004341885.1_ASM434188v1_genomic.fna/cds.fna -a GCF_004341885.1_ASM434188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:04,856] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:04,857] [INFO] Task started: HMMsearch
[2024-01-24 14:20:04,857] [INFO] Running command: hmmsearch --tblout GCF_004341885.1_ASM434188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference/reference_markers.hmm GCF_004341885.1_ASM434188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:05,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:05,209] [INFO] Found 6/6 markers.
[2024-01-24 14:20:05,260] [INFO] Query marker FASTA was written to GCF_004341885.1_ASM434188v1_genomic.fna/markers.fasta
[2024-01-24 14:20:05,260] [INFO] Task started: Blastn
[2024-01-24 14:20:05,260] [INFO] Running command: blastn -query GCF_004341885.1_ASM434188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference/reference_markers.fasta -out GCF_004341885.1_ASM434188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:06,222] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:06,225] [INFO] Selected 24 target genomes.
[2024-01-24 14:20:06,225] [INFO] Target genome list was writen to GCF_004341885.1_ASM434188v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:06,236] [INFO] Task started: fastANI
[2024-01-24 14:20:06,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg368f677a-5b62-44e2-a73e-7f0bb2ac1f5f/GCF_004341885.1_ASM434188v1_genomic.fna.gz --refList GCF_004341885.1_ASM434188v1_genomic.fna/target_genomes.txt --output GCF_004341885.1_ASM434188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:31,396] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:31,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:31,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:31,409] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:31,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:31,410] [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
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	100.0	2141	2146	95	conclusive
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	94.0724	1660	2146	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	88.0469	1209	2146	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	88.0212	1163	2146	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	88.0045	1174	2146	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	86.9602	1446	2146	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	86.5975	1326	2146	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	86.1444	1159	2146	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	85.9579	1162	2146	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	85.9122	1153	2146	95	below_threshold
Variibacter gotjawalensis	strain=GJW-30	GCA_002355335.1	1333996	1333996	type	True	76.8337	238	2146	95	below_threshold
Variibacter gotjawalensis	strain=DSM 29671	GCA_004216635.1	1333996	1333996	type	True	76.8148	241	2146	95	below_threshold
Variibacter gotjawalensis	strain=CECT 8514	GCA_011761465.1	1333996	1333996	type	True	76.8082	237	2146	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	76.0361	174	2146	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	75.5131	130	2146	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	75.5025	140	2146	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	75.338	93	2146	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	75.2461	189	2146	95	below_threshold
Xanthomonas prunicola	strain=CFBP 8353	GCA_002846205.1	2053930	2053930	type	True	75.2255	83	2146	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	75.0719	116	2146	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:31,411] [INFO] DFAST Taxonomy check result was written to GCF_004341885.1_ASM434188v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:31,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:31,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:31,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference/checkm_data
[2024-01-24 14:20:31,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:31,472] [INFO] Task started: CheckM
[2024-01-24 14:20:31,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341885.1_ASM434188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341885.1_ASM434188v1_genomic.fna/checkm_input GCF_004341885.1_ASM434188v1_genomic.fna/checkm_result
[2024-01-24 14:21:25,995] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:25,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:26,010] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:26,010] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:26,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341885.1_ASM434188v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:26,011] [INFO] Task started: Blastn
[2024-01-24 14:21:26,011] [INFO] Running command: blastn -query GCF_004341885.1_ASM434188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf205ef9d-c3c6-4879-ac3b-813eca9ee5b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341885.1_ASM434188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:27,842] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:27,845] [INFO] Selected 18 target genomes.
[2024-01-24 14:21:27,845] [INFO] Target genome list was writen to GCF_004341885.1_ASM434188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:27,856] [INFO] Task started: fastANI
[2024-01-24 14:21:27,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg368f677a-5b62-44e2-a73e-7f0bb2ac1f5f/GCF_004341885.1_ASM434188v1_genomic.fna.gz --refList GCF_004341885.1_ASM434188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341885.1_ASM434188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:48,002] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:48,012] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:48,012] [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_004341885.1	s__Shinella granuli	100.0	2141	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	conclusive
GCF_001262505.1	s__Shinella sp001262505	91.1354	1638	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_016839145.1	s__Shinella sp016839145	88.1915	1285	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	88.0557	1208	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	88.0429	1161	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	87.9609	1252	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827055.1	s__Shinella kummerowiae	86.9447	1448	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713395.1	s__Shinella sp001713395	86.889	1427	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470805.1	s__Rhizobium sp900470805	79.9187	764	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	77.9095	170	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473415.1	s__Bosea sp900473415	77.5275	451	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355335.1	s__Variibacter gotjawalensis	76.8438	238	2146	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Variibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	75.3899	163	2146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
GCF_004361065.1	s__Lysobacter terrigena	75.3542	94	2146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851915.1	s__Pseudoxanthomonas sp014851915	75.1788	177	2146	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526565.1	s__WYBL01 sp011526565	75.0723	189	2146	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Fen-336;f__Fen-336;g__WYBL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:48,013] [INFO] GTDB search result was written to GCF_004341885.1_ASM434188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:48,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:48,017] [INFO] DFAST_QC result json was written to GCF_004341885.1_ASM434188v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:48,017] [INFO] DFAST_QC completed!
[2024-01-24 14:21:48,017] [INFO] Total running time: 0h2m2s