[2024-01-24 11:05:25,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference
[2024-01-24 11:05:26,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,896] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,897] [INFO] Running command: gunzip -c /var/lib/cwl/stg974dc9d8-d8f4-4a0e-928d-ce033042ff7c/GCF_902859585.1_LMG_26690_genomic.fna.gz | prodigal -d GCF_902859585.1_LMG_26690_genomic.fna/cds.fna -a GCF_902859585.1_LMG_26690_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:46,661] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:46,662] [INFO] Task started: HMMsearch
[2024-01-24 11:05:46,662] [INFO] Running command: hmmsearch --tblout GCF_902859585.1_LMG_26690_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference/reference_markers.hmm GCF_902859585.1_LMG_26690_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:47,015] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:47,016] [INFO] Found 6/6 markers.
[2024-01-24 11:05:47,067] [INFO] Query marker FASTA was written to GCF_902859585.1_LMG_26690_genomic.fna/markers.fasta
[2024-01-24 11:05:47,067] [INFO] Task started: Blastn
[2024-01-24 11:05:47,067] [INFO] Running command: blastn -query GCF_902859585.1_LMG_26690_genomic.fna/markers.fasta -db /var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference/reference_markers.fasta -out GCF_902859585.1_LMG_26690_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:48,120] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:48,124] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:48,125] [INFO] Target genome list was writen to GCF_902859585.1_LMG_26690_genomic.fna/target_genomes.txt
[2024-01-24 11:05:48,132] [INFO] Task started: fastANI
[2024-01-24 11:05:48,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg974dc9d8-d8f4-4a0e-928d-ce033042ff7c/GCF_902859585.1_LMG_26690_genomic.fna.gz --refList GCF_902859585.1_LMG_26690_genomic.fna/target_genomes.txt --output GCF_902859585.1_LMG_26690_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:16,317] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:16,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:16,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:16,339] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:16,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:16,340] [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
Achromobacter animicus	strain=LMG 26690	GCA_902859585.1	1389935	1389935	type	True	100.0	2005	2007	95	conclusive
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	90.5215	1707	2007	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	85.8207	1372	2007	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	85.7308	1318	2007	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	85.631	1338	2007	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	85.6155	1344	2007	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	85.6121	1351	2007	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	85.5668	1385	2007	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	85.4706	1448	2007	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	85.4607	1455	2007	95	below_threshold
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	85.4325	1443	2007	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	85.3902	1352	2007	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	85.3677	1344	2007	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	85.3099	1380	2007	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.2386	1389	2007	95	below_threshold
Achromobacter agilis	strain=LMG 3411	GCA_900496965.1	1353888	1353888	type	True	85.1696	1359	2007	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.7085	1364	2007	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.9743	816	2007	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7704	319	2007	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	77.2894	382	2007	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:16,341] [INFO] DFAST Taxonomy check result was written to GCF_902859585.1_LMG_26690_genomic.fna/tc_result.tsv
[2024-01-24 11:06:16,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:16,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:16,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference/checkm_data
[2024-01-24 11:06:16,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:16,403] [INFO] Task started: CheckM
[2024-01-24 11:06:16,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859585.1_LMG_26690_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859585.1_LMG_26690_genomic.fna/checkm_input GCF_902859585.1_LMG_26690_genomic.fna/checkm_result
[2024-01-24 11:07:15,130] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:15,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:15,155] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:15,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:15,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859585.1_LMG_26690_genomic.fna/markers.fasta)
[2024-01-24 11:07:15,156] [INFO] Task started: Blastn
[2024-01-24 11:07:15,157] [INFO] Running command: blastn -query GCF_902859585.1_LMG_26690_genomic.fna/markers.fasta -db /var/lib/cwl/stg98711799-6863-4263-9a4a-307531de0ca6/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859585.1_LMG_26690_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:17,224] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:17,228] [INFO] Selected 7 target genomes.
[2024-01-24 11:07:17,228] [INFO] Target genome list was writen to GCF_902859585.1_LMG_26690_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:17,277] [INFO] Task started: fastANI
[2024-01-24 11:07:17,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg974dc9d8-d8f4-4a0e-928d-ce033042ff7c/GCF_902859585.1_LMG_26690_genomic.fna.gz --refList GCF_902859585.1_LMG_26690_genomic.fna/target_genomes_gtdb.txt --output GCF_902859585.1_LMG_26690_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:28,501] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:28,512] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:28,513] [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_902859585.1	s__Achromobacter animicus	100.0	2005	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.58	96.10	0.93	0.89	8	conclusive
GCA_003454835.1	s__Achromobacter sp003454835	93.5076	1086	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966795.1	s__Achromobacter spanius_D	93.5054	1836	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	95.32	95.32	0.92	0.92	2	-
GCF_902859725.1	s__Achromobacter mucicolens	90.5215	1707	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.28	95.42	0.92	0.89	13	-
GCF_900156745.1	s__Achromobacter sp900156745	88.9505	1624	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.81	97.81	0.91	0.91	2	-
GCF_000236785.1	s__Achromobacter arsenitoxydans	87.5965	1531	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428845.1	s__Achromobacter sp001428845	86.6496	1521	2007	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:28,514] [INFO] GTDB search result was written to GCF_902859585.1_LMG_26690_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:28,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:28,518] [INFO] DFAST_QC result json was written to GCF_902859585.1_LMG_26690_genomic.fna/dqc_result.json
[2024-01-24 11:07:28,519] [INFO] DFAST_QC completed!
[2024-01-24 11:07:28,519] [INFO] Total running time: 0h2m3s