[2024-01-24 14:05:31,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference
[2024-01-24 14:05:32,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,845] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bdf8118-88f8-4ccc-bbea-1874c9afe162/GCF_003201815.1_ASM320181v1_genomic.fna.gz | prodigal -d GCF_003201815.1_ASM320181v1_genomic.fna/cds.fna -a GCF_003201815.1_ASM320181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:53,268] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:53,268] [INFO] Task started: HMMsearch
[2024-01-24 14:05:53,268] [INFO] Running command: hmmsearch --tblout GCF_003201815.1_ASM320181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference/reference_markers.hmm GCF_003201815.1_ASM320181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:53,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:53,654] [INFO] Found 6/6 markers.
[2024-01-24 14:05:53,706] [INFO] Query marker FASTA was written to GCF_003201815.1_ASM320181v1_genomic.fna/markers.fasta
[2024-01-24 14:05:53,707] [INFO] Task started: Blastn
[2024-01-24 14:05:53,707] [INFO] Running command: blastn -query GCF_003201815.1_ASM320181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference/reference_markers.fasta -out GCF_003201815.1_ASM320181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:54,475] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:54,478] [INFO] Selected 16 target genomes.
[2024-01-24 14:05:54,478] [INFO] Target genome list was writen to GCF_003201815.1_ASM320181v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:54,484] [INFO] Task started: fastANI
[2024-01-24 14:05:54,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bdf8118-88f8-4ccc-bbea-1874c9afe162/GCF_003201815.1_ASM320181v1_genomic.fna.gz --refList GCF_003201815.1_ASM320181v1_genomic.fna/target_genomes.txt --output GCF_003201815.1_ASM320181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:10,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:10,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:10,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:10,843] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:10,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:10,843] [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 pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	100.0	2111	2114	95	conclusive
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	86.6407	1663	2114	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	82.3078	1215	2114	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.9014	331	2114	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	78.8013	438	2114	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	78.7588	418	2114	95	below_threshold
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	78.7399	406	2114	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	78.6419	439	2114	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	78.63	388	2114	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.8969	203	2114	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	76.8427	179	2114	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.7061	152	2114	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.654	145	2114	95	below_threshold
Duganella phyllosphaerae	strain=T54	GCA_001758785.1	762836	762836	type	True	76.4833	150	2114	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.3901	114	2114	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	76.3425	104	2114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:10,845] [INFO] DFAST Taxonomy check result was written to GCF_003201815.1_ASM320181v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:10,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:10,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:10,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference/checkm_data
[2024-01-24 14:06:10,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:10,911] [INFO] Task started: CheckM
[2024-01-24 14:06:10,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201815.1_ASM320181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201815.1_ASM320181v1_genomic.fna/checkm_input GCF_003201815.1_ASM320181v1_genomic.fna/checkm_result
[2024-01-24 14:07:12,115] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:12,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:12,135] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:12,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:12,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201815.1_ASM320181v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:12,137] [INFO] Task started: Blastn
[2024-01-24 14:07:12,137] [INFO] Running command: blastn -query GCF_003201815.1_ASM320181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6ff45d-29e5-44df-a256-fedc74cd82ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201815.1_ASM320181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:13,299] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:13,302] [INFO] Selected 6 target genomes.
[2024-01-24 14:07:13,303] [INFO] Target genome list was writen to GCF_003201815.1_ASM320181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:13,308] [INFO] Task started: fastANI
[2024-01-24 14:07:13,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bdf8118-88f8-4ccc-bbea-1874c9afe162/GCF_003201815.1_ASM320181v1_genomic.fna.gz --refList GCF_003201815.1_ASM320181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201815.1_ASM320181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:23,826] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:23,836] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:23,837] [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_003201815.1	s__Undibacterium pigrum	100.0	2111	2114	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_014284125.1	s__Undibacterium sp014284125	86.6389	1664	2114	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	86.5261	1616	2114	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	86.3946	1573	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200895.1	s__Undibacterium sp016200895	86.0188	1399	2114	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	82.282	1217	2114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:23,838] [INFO] GTDB search result was written to GCF_003201815.1_ASM320181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:23,839] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:23,844] [INFO] DFAST_QC result json was written to GCF_003201815.1_ASM320181v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:23,844] [INFO] DFAST_QC completed!
[2024-01-24 14:07:23,844] [INFO] Total running time: 0h1m52s