[2024-01-24 10:47:06,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,555] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,555] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a6673ff-4a5a-40aa-87fc-d1d3daa88961/GCF_014284235.1_ASM1428423v1_genomic.fna.gz | prodigal -d GCF_014284235.1_ASM1428423v1_genomic.fna/cds.fna -a GCF_014284235.1_ASM1428423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,468] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,469] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,469] [INFO] Running command: hmmsearch --tblout GCF_014284235.1_ASM1428423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference/reference_markers.hmm GCF_014284235.1_ASM1428423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,763] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,807] [INFO] Query marker FASTA was written to GCF_014284235.1_ASM1428423v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,808] [INFO] Task started: Blastn
[2024-01-24 10:47:24,808] [INFO] Running command: blastn -query GCF_014284235.1_ASM1428423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference/reference_markers.fasta -out GCF_014284235.1_ASM1428423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,536] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,540] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:25,540] [INFO] Target genome list was writen to GCF_014284235.1_ASM1428423v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,569] [INFO] Task started: fastANI
[2024-01-24 10:47:25,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a6673ff-4a5a-40aa-87fc-d1d3daa88961/GCF_014284235.1_ASM1428423v1_genomic.fna.gz --refList GCF_014284235.1_ASM1428423v1_genomic.fna/target_genomes.txt --output GCF_014284235.1_ASM1428423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:40,678] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:40,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:40,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:40,692] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:40,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:40,692] [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 curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	100.0	1400	1401	95	conclusive
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	93.1355	1217	1401	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	89.8776	1174	1401	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	79.4805	481	1401	95	below_threshold
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	79.2336	451	1401	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.7594	480	1401	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	78.697	426	1401	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	78.6485	446	1401	95	below_threshold
Undibacterium luofuense	strain=LFS511W	GCA_018139685.1	2828733	2828733	type	True	78.4156	453	1401	95	below_threshold
Undibacterium squillarum	strain=KCTC 23917	GCA_014652435.1	1131567	1131567	type	True	78.3435	448	1401	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.7238	140	1401	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	76.6026	123	1401	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.487	89	1401	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	76.4418	124	1401	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.4213	133	1401	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.2314	128	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:40,695] [INFO] DFAST Taxonomy check result was written to GCF_014284235.1_ASM1428423v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:40,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:40,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:40,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference/checkm_data
[2024-01-24 10:47:40,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:40,737] [INFO] Task started: CheckM
[2024-01-24 10:47:40,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284235.1_ASM1428423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284235.1_ASM1428423v1_genomic.fna/checkm_input GCF_014284235.1_ASM1428423v1_genomic.fna/checkm_result
[2024-01-24 10:48:19,749] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:19,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:19,764] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:19,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:19,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284235.1_ASM1428423v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:19,764] [INFO] Task started: Blastn
[2024-01-24 10:48:19,765] [INFO] Running command: blastn -query GCF_014284235.1_ASM1428423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf6eb03c-13ef-4344-b5cf-c4bf99df4fac/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284235.1_ASM1428423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:20,922] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:20,925] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:20,925] [INFO] Target genome list was writen to GCF_014284235.1_ASM1428423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:20,951] [INFO] Task started: fastANI
[2024-01-24 10:48:20,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a6673ff-4a5a-40aa-87fc-d1d3daa88961/GCF_014284235.1_ASM1428423v1_genomic.fna.gz --refList GCF_014284235.1_ASM1428423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284235.1_ASM1428423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:31,897] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:31,907] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:31,907] [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_014284235.1	s__Undibacterium sp014284235	100.0	1400	1401	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_010078235.1	s__Undibacterium crateris	93.1355	1217	1401	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	89.8776	1174	1401	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	79.4618	482	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377855.1	s__Undibacterium oligocarboniphilum	79.2439	451	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009937955.1	s__Undibacterium sp009937955	78.7607	438	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284125.1	s__Undibacterium sp014284125	78.7093	426	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201815.1	s__Undibacterium pigrum	78.6581	445	1401	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	78.6536	451	1401	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	78.515	370	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139685.1	s__Undibacterium sp018139685	78.4063	453	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427305.1	s__Pseudoduganella sp001427305	76.5794	141	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:31,909] [INFO] GTDB search result was written to GCF_014284235.1_ASM1428423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:31,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:31,914] [INFO] DFAST_QC result json was written to GCF_014284235.1_ASM1428423v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:31,914] [INFO] DFAST_QC completed!
[2024-01-24 10:48:31,914] [INFO] Total running time: 0h1m25s