[2024-01-24 15:18:51,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,890] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference
[2024-01-24 15:18:54,594] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,595] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,596] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5df3ce0-e8f7-46df-ac66-432b75497e42/GCF_014284155.1_ASM1428415v1_genomic.fna.gz | prodigal -d GCF_014284155.1_ASM1428415v1_genomic.fna/cds.fna -a GCF_014284155.1_ASM1428415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:08,069] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:08,070] [INFO] Task started: HMMsearch
[2024-01-24 15:19:08,070] [INFO] Running command: hmmsearch --tblout GCF_014284155.1_ASM1428415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference/reference_markers.hmm GCF_014284155.1_ASM1428415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:08,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:08,393] [INFO] Found 6/6 markers.
[2024-01-24 15:19:08,434] [INFO] Query marker FASTA was written to GCF_014284155.1_ASM1428415v1_genomic.fna/markers.fasta
[2024-01-24 15:19:08,434] [INFO] Task started: Blastn
[2024-01-24 15:19:08,434] [INFO] Running command: blastn -query GCF_014284155.1_ASM1428415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference/reference_markers.fasta -out GCF_014284155.1_ASM1428415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:09,220] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:09,229] [INFO] Selected 17 target genomes.
[2024-01-24 15:19:09,229] [INFO] Target genome list was writen to GCF_014284155.1_ASM1428415v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:09,249] [INFO] Task started: fastANI
[2024-01-24 15:19:09,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5df3ce0-e8f7-46df-ac66-432b75497e42/GCF_014284155.1_ASM1428415v1_genomic.fna.gz --refList GCF_014284155.1_ASM1428415v1_genomic.fna/target_genomes.txt --output GCF_014284155.1_ASM1428415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:23,516] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:23,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:23,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:23,527] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:23,527] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:23,528] [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 nitidum	strain=LX22W	GCA_014284155.1	2762298	2762298	type	True	100.0	1443	1443	95	conclusive
Undibacterium fentianense	strain=FT137W	GCA_018139545.1	2828728	2828728	type	True	80.2592	364	1443	95	below_threshold
Undibacterium macrobrachii	strain=KCTC 23916	GCA_014652415.1	1119058	1119058	type	True	80.0734	387	1443	95	below_threshold
Undibacterium seohonense	strain=KACC 16656	GCA_014284305.1	1344950	1344950	type	True	80.0102	380	1443	95	below_threshold
Undibacterium baiyunense	strain=BYS107W	GCA_018139645.1	2828731	2828731	type	True	79.9963	391	1443	95	below_threshold
Undibacterium flavidum	strain=LX15W	GCA_014284175.1	2762297	2762297	type	True	79.9143	368	1443	95	below_threshold
Undibacterium amnicola	strain=KCTC 52442	GCA_014284275.1	1834038	1834038	type	True	79.5629	395	1443	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.5943	179	1443	95	below_threshold
Undibacterium terreum	strain=CGMCC 1.10998	GCA_014636315.1	1224302	1224302	type	True	78.256	121	1443	95	below_threshold
Glaciimonas soli	strain=GS1	GCA_009497155.1	2590999	2590999	type	True	77.4937	93	1443	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.2588	63	1443	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	76.5974	65	1443	95	below_threshold
Duganella guangzhouensis	strain=FT80W	GCA_009674535.1	2666084	2666084	type	True	76.4805	60	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:23,529] [INFO] DFAST Taxonomy check result was written to GCF_014284155.1_ASM1428415v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:23,530] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:23,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:23,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference/checkm_data
[2024-01-24 15:19:23,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:23,573] [INFO] Task started: CheckM
[2024-01-24 15:19:23,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284155.1_ASM1428415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284155.1_ASM1428415v1_genomic.fna/checkm_input GCF_014284155.1_ASM1428415v1_genomic.fna/checkm_result
[2024-01-24 15:20:04,152] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:04,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:04,171] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:04,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:04,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284155.1_ASM1428415v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:04,172] [INFO] Task started: Blastn
[2024-01-24 15:20:04,173] [INFO] Running command: blastn -query GCF_014284155.1_ASM1428415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc0fc56d-5a54-4fae-aba3-f3005cd9efd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284155.1_ASM1428415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:05,332] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:05,336] [INFO] Selected 12 target genomes.
[2024-01-24 15:20:05,336] [INFO] Target genome list was writen to GCF_014284155.1_ASM1428415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:05,346] [INFO] Task started: fastANI
[2024-01-24 15:20:05,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5df3ce0-e8f7-46df-ac66-432b75497e42/GCF_014284155.1_ASM1428415v1_genomic.fna.gz --refList GCF_014284155.1_ASM1428415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284155.1_ASM1428415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:15,191] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:15,203] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:15,204] [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_014284115.1	s__Undibacterium sp014284115	99.9992	1442	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018139545.1	s__Undibacterium sp018139545	80.2553	365	1443	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	80.0734	387	1443	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	80.0208	380	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139645.1	s__Undibacterium sp018139645	79.9966	391	1443	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	79.9114	369	1443	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	79.5939	393	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200845.1	s__Undibacterium sp016200845	79.0008	250	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636315.1	s__Undibacterium terreum	78.2257	122	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584185.1	s__Collimonas pratensis	77.2804	64	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	98.16	98.11	0.88	0.88	3	-
GCF_001189915.1	s__Herbaspirillum autotrophicum	76.5974	65	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:15,208] [INFO] GTDB search result was written to GCF_014284155.1_ASM1428415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:15,209] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:15,212] [INFO] DFAST_QC result json was written to GCF_014284155.1_ASM1428415v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:15,212] [INFO] DFAST_QC completed!
[2024-01-24 15:20:15,212] [INFO] Total running time: 0h1m23s