[2024-01-25 18:03:05,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:05,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:05,570] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference
[2024-01-25 18:03:06,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:06,670] [INFO] Task started: Prodigal
[2024-01-25 18:03:06,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg316d3c50-f4f5-49a6-859a-612b0e6e99b6/GCF_010078235.1_ASM1007823v1_genomic.fna.gz | prodigal -d GCF_010078235.1_ASM1007823v1_genomic.fna/cds.fna -a GCF_010078235.1_ASM1007823v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:17,512] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:17,512] [INFO] Task started: HMMsearch
[2024-01-25 18:03:17,512] [INFO] Running command: hmmsearch --tblout GCF_010078235.1_ASM1007823v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference/reference_markers.hmm GCF_010078235.1_ASM1007823v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:17,756] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:17,757] [INFO] Found 6/6 markers.
[2024-01-25 18:03:17,794] [INFO] Query marker FASTA was written to GCF_010078235.1_ASM1007823v1_genomic.fna/markers.fasta
[2024-01-25 18:03:17,794] [INFO] Task started: Blastn
[2024-01-25 18:03:17,794] [INFO] Running command: blastn -query GCF_010078235.1_ASM1007823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference/reference_markers.fasta -out GCF_010078235.1_ASM1007823v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:18,459] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:18,462] [INFO] Selected 15 target genomes.
[2024-01-25 18:03:18,462] [INFO] Target genome list was writen to GCF_010078235.1_ASM1007823v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:18,479] [INFO] Task started: fastANI
[2024-01-25 18:03:18,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg316d3c50-f4f5-49a6-859a-612b0e6e99b6/GCF_010078235.1_ASM1007823v1_genomic.fna.gz --refList GCF_010078235.1_ASM1007823v1_genomic.fna/target_genomes.txt --output GCF_010078235.1_ASM1007823v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:33,229] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:33,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:33,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:33,238] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:33,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:33,239] [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
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	100.0	1418	1418	95	conclusive
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	93.1778	1227	1418	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	90.0475	1169	1418	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	79.5723	478	1418	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	79.3431	455	1418	95	below_threshold
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	79.1646	452	1418	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	78.7343	455	1418	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	78.6748	415	1418	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.5221	479	1418	95	below_threshold
Undibacterium luofuense	strain=LFS511W	GCA_018139685.1	2828733	2828733	type	True	78.5181	456	1418	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.0645	127	1418	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.1202	142	1418	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	75.9388	134	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:33,240] [INFO] DFAST Taxonomy check result was written to GCF_010078235.1_ASM1007823v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:33,240] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:33,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:33,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference/checkm_data
[2024-01-25 18:03:33,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:33,285] [INFO] Task started: CheckM
[2024-01-25 18:03:33,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010078235.1_ASM1007823v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010078235.1_ASM1007823v1_genomic.fna/checkm_input GCF_010078235.1_ASM1007823v1_genomic.fna/checkm_result
[2024-01-25 18:04:08,907] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:08,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:08,929] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:08,929] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:08,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010078235.1_ASM1007823v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:08,931] [INFO] Task started: Blastn
[2024-01-25 18:04:08,931] [INFO] Running command: blastn -query GCF_010078235.1_ASM1007823v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5ce356a-7339-408e-9eac-5b4d5b8e03c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_010078235.1_ASM1007823v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:10,105] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:10,110] [INFO] Selected 11 target genomes.
[2024-01-25 18:04:10,111] [INFO] Target genome list was writen to GCF_010078235.1_ASM1007823v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:10,127] [INFO] Task started: fastANI
[2024-01-25 18:04:10,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg316d3c50-f4f5-49a6-859a-612b0e6e99b6/GCF_010078235.1_ASM1007823v1_genomic.fna.gz --refList GCF_010078235.1_ASM1007823v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010078235.1_ASM1007823v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:20,802] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:20,809] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:20,809] [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_010078235.1	s__Undibacterium crateris	100.0	1418	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014284235.1	s__Undibacterium sp014284235	93.1778	1227	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284365.1	s__Undibacterium sp014284365	90.0475	1169	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014284195.1	s__Undibacterium sp014284195	79.5785	477	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699135.1	s__Undibacterium aquatile	79.3753	452	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
GCF_013377855.1	s__Undibacterium oligocarboniphilum	79.1443	454	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003201815.1	s__Undibacterium pigrum	78.7251	456	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937955.1	s__Undibacterium sp009937955	78.6034	440	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937975.1	s__Undibacterium sp009937975	78.5273	453	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284335.1	s__Undibacterium sp014284335	78.5061	481	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016196925.1	s__Undibacterium sp016196925	78.4397	374	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:20,811] [INFO] GTDB search result was written to GCF_010078235.1_ASM1007823v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:20,811] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:20,815] [INFO] DFAST_QC result json was written to GCF_010078235.1_ASM1007823v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:20,815] [INFO] DFAST_QC completed!
[2024-01-25 18:04:20,815] [INFO] Total running time: 0h1m15s