[2024-01-24 11:34:41,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference
[2024-01-24 11:34:42,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,792] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,792] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cebd61b-f524-4d07-9fa3-a1f2595b69c5/GCF_002976435.1_ASM297643v1_genomic.fna.gz | prodigal -d GCF_002976435.1_ASM297643v1_genomic.fna/cds.fna -a GCF_002976435.1_ASM297643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,551] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,552] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,552] [INFO] Running command: hmmsearch --tblout GCF_002976435.1_ASM297643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference/reference_markers.hmm GCF_002976435.1_ASM297643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:57,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:57,947] [INFO] Found 6/6 markers.
[2024-01-24 11:34:58,002] [INFO] Query marker FASTA was written to GCF_002976435.1_ASM297643v1_genomic.fna/markers.fasta
[2024-01-24 11:34:58,003] [INFO] Task started: Blastn
[2024-01-24 11:34:58,003] [INFO] Running command: blastn -query GCF_002976435.1_ASM297643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference/reference_markers.fasta -out GCF_002976435.1_ASM297643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,718] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,721] [INFO] Selected 21 target genomes.
[2024-01-24 11:34:58,721] [INFO] Target genome list was writen to GCF_002976435.1_ASM297643v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,739] [INFO] Task started: fastANI
[2024-01-24 11:34:58,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cebd61b-f524-4d07-9fa3-a1f2595b69c5/GCF_002976435.1_ASM297643v1_genomic.fna.gz --refList GCF_002976435.1_ASM297643v1_genomic.fna/target_genomes.txt --output GCF_002976435.1_ASM297643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:14,910] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:14,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:14,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:14,927] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:14,927] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:14,927] [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
Solimicrobium silvestre	strain=S20-91	GCA_002976435.1	2099400	2099400	type	True	100.0	1713	1716	95	conclusive
Sapientia aquatica	strain=SA-152	GCA_004358105.1	1549640	1549640	type	True	79.0896	396	1716	95	below_threshold
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	77.8555	124	1716	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	77.8482	114	1716	95	below_threshold
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	77.7748	127	1716	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	77.7607	139	1716	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	77.7451	133	1716	95	below_threshold
Undibacterium nitidum	strain=LX22W	GCA_014284155.1	2762298	2762298	type	True	77.7199	104	1716	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	77.6933	129	1716	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	77.4964	114	1716	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	77.4642	129	1716	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	77.3565	106	1716	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	77.29	126	1716	95	below_threshold
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	77.2541	105	1716	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	77.2466	126	1716	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	77.2278	106	1716	95	below_threshold
Undibacterium macrobrachii	strain=KCTC 23916	GCA_014652415.1	1119058	1119058	type	True	77.1655	121	1716	95	below_threshold
Undibacterium luofuense	strain=LFS511W	GCA_018139685.1	2828733	2828733	type	True	76.8785	102	1716	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	76.8412	96	1716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:14,929] [INFO] DFAST Taxonomy check result was written to GCF_002976435.1_ASM297643v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:14,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:14,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:14,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference/checkm_data
[2024-01-24 11:35:14,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:14,985] [INFO] Task started: CheckM
[2024-01-24 11:35:14,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002976435.1_ASM297643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002976435.1_ASM297643v1_genomic.fna/checkm_input GCF_002976435.1_ASM297643v1_genomic.fna/checkm_result
[2024-01-24 11:36:00,232] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:00,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:00,257] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:00,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:00,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002976435.1_ASM297643v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:00,259] [INFO] Task started: Blastn
[2024-01-24 11:36:00,259] [INFO] Running command: blastn -query GCF_002976435.1_ASM297643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb90fed57-d2ec-4e70-ba14-31391281c286/dqc_reference/reference_markers_gtdb.fasta -out GCF_002976435.1_ASM297643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:01,420] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:01,424] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:01,425] [INFO] Target genome list was writen to GCF_002976435.1_ASM297643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:01,440] [INFO] Task started: fastANI
[2024-01-24 11:36:01,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cebd61b-f524-4d07-9fa3-a1f2595b69c5/GCF_002976435.1_ASM297643v1_genomic.fna.gz --refList GCF_002976435.1_ASM297643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002976435.1_ASM297643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:14,835] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:14,857] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:14,857] [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_002976435.1	s__Solimicrobium silvestre	100.0	1713	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004358105.1	s__Solimicrobium aquaticum	79.0838	396	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862415.1	s__Solimicrobium sp903862415	78.0739	321	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_018139565.1	s__Undibacterium sp018139565	77.8555	124	1716	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	77.8482	114	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	96.61	96.29	0.93	0.93	4	-
GCF_014284305.1	s__Undibacterium seohonense	77.7842	128	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284255.1	s__Undibacterium jejuense	77.7568	140	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284175.1	s__Undibacterium sp014284175	77.7197	147	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003955735.1	s__Undibacterium parvum	77.7061	145	1716	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	77.624	134	1716	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	77.4704	128	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893945.1	s__Solimicrobium sp903893945	77.3499	182	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	99.85	99.85	0.96	0.96	2	-
GCF_003293745.1	s__Herminiimonas fonticola	77.2972	105	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018305005.1	s__Collimonas sp018305005	76.845	97	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192645.1	s__Herbaspirillum sp014192645	76.836	89	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003852535.1	s__Herminiimonas sp003852535	76.8057	95	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464355.1	s__Herminiimonas sp001464355	76.7333	107	1716	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,859] [INFO] GTDB search result was written to GCF_002976435.1_ASM297643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:14,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:14,863] [INFO] DFAST_QC result json was written to GCF_002976435.1_ASM297643v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:14,863] [INFO] DFAST_QC completed!
[2024-01-24 11:36:14,863] [INFO] Total running time: 0h1m33s