[2024-01-24 11:58:55,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference
[2024-01-24 11:58:56,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:56,488] [INFO] Task started: Prodigal
[2024-01-24 11:58:56,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d2f59ad-18ec-45b3-8626-66733122bcf1/GCF_014284255.1_ASM1428425v1_genomic.fna.gz | prodigal -d GCF_014284255.1_ASM1428425v1_genomic.fna/cds.fna -a GCF_014284255.1_ASM1428425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:08,763] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:08,763] [INFO] Task started: HMMsearch
[2024-01-24 11:59:08,764] [INFO] Running command: hmmsearch --tblout GCF_014284255.1_ASM1428425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference/reference_markers.hmm GCF_014284255.1_ASM1428425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:09,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:09,124] [INFO] Found 6/6 markers.
[2024-01-24 11:59:09,169] [INFO] Query marker FASTA was written to GCF_014284255.1_ASM1428425v1_genomic.fna/markers.fasta
[2024-01-24 11:59:09,169] [INFO] Task started: Blastn
[2024-01-24 11:59:09,169] [INFO] Running command: blastn -query GCF_014284255.1_ASM1428425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference/reference_markers.fasta -out GCF_014284255.1_ASM1428425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:09,866] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:09,877] [INFO] Selected 17 target genomes.
[2024-01-24 11:59:09,878] [INFO] Target genome list was writen to GCF_014284255.1_ASM1428425v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:09,885] [INFO] Task started: fastANI
[2024-01-24 11:59:09,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2f59ad-18ec-45b3-8626-66733122bcf1/GCF_014284255.1_ASM1428425v1_genomic.fna.gz --refList GCF_014284255.1_ASM1428425v1_genomic.fna/target_genomes.txt --output GCF_014284255.1_ASM1428425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:24,260] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:24,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:24,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:24,284] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:24,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:24,285] [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 jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	100.0	1450	1451	95	conclusive
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	79.2518	384	1451	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	79.1619	364	1451	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	79.1327	399	1451	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	79.0548	320	1451	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	78.9234	364	1451	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	78.7881	343	1451	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	78.7394	328	1451	95	below_threshold
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	78.6221	330	1451	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	78.5763	342	1451	95	below_threshold
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	78.3473	207	1451	95	below_threshold
Undibacterium amnicola	strain=KCTC 52442	GCA_014284275.1	1834038	1834038	type	True	78.2299	190	1451	95	below_threshold
Undibacterium macrobrachii	strain=KCTC 23916	GCA_014652415.1	1119058	1119058	type	True	78.0249	202	1451	95	below_threshold
Undibacterium terreum	strain=CGMCC 1.10998	GCA_014636315.1	1224302	1224302	type	True	78.0103	201	1451	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.8403	71	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:24,287] [INFO] DFAST Taxonomy check result was written to GCF_014284255.1_ASM1428425v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:24,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:24,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:24,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference/checkm_data
[2024-01-24 11:59:24,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:24,380] [INFO] Task started: CheckM
[2024-01-24 11:59:24,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284255.1_ASM1428425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284255.1_ASM1428425v1_genomic.fna/checkm_input GCF_014284255.1_ASM1428425v1_genomic.fna/checkm_result
[2024-01-24 12:00:03,092] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:03,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:03,111] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:03,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:03,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284255.1_ASM1428425v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:03,112] [INFO] Task started: Blastn
[2024-01-24 12:00:03,112] [INFO] Running command: blastn -query GCF_014284255.1_ASM1428425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c385a6d-d017-4af3-9468-eb7e15fcfa33/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284255.1_ASM1428425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:04,349] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:04,354] [INFO] Selected 17 target genomes.
[2024-01-24 12:00:04,354] [INFO] Target genome list was writen to GCF_014284255.1_ASM1428425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:04,375] [INFO] Task started: fastANI
[2024-01-24 12:00:04,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d2f59ad-18ec-45b3-8626-66733122bcf1/GCF_014284255.1_ASM1428425v1_genomic.fna.gz --refList GCF_014284255.1_ASM1428425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284255.1_ASM1428425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:17,547] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:17,560] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:17,560] [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_014284255.1	s__Undibacterium jejuense	100.0	1450	1451	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_018139565.1	s__Undibacterium sp018139565	79.2546	384	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010078235.1	s__Undibacterium crateris	79.1737	364	1451	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	79.139	398	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
GCF_014284365.1	s__Undibacterium sp014284365	79.0563	321	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014284235.1	s__Undibacterium sp014284235	78.9339	364	1451	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	78.8772	325	1451	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	78.7955	343	1451	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	78.7394	328	1451	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	78.7322	305	1451	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	78.6176	331	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014284195.1	s__Undibacterium sp014284195	78.5831	341	1451	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	78.5032	341	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284305.1	s__Undibacterium seohonense	78.3607	207	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284275.1	s__Undibacterium amnicola	78.2335	191	1451	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652415.1	s__Undibacterium macrobrachii	78.0249	202	1451	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 12:00:17,562] [INFO] GTDB search result was written to GCF_014284255.1_ASM1428425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:17,563] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:17,567] [INFO] DFAST_QC result json was written to GCF_014284255.1_ASM1428425v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:17,567] [INFO] DFAST_QC completed!
[2024-01-24 12:00:17,567] [INFO] Total running time: 0h1m22s