[2024-01-24 12:37:07,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:07,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:07,281] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference
[2024-01-24 12:37:08,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:08,560] [INFO] Task started: Prodigal
[2024-01-24 12:37:08,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg785b4663-434c-45bc-b5c9-abbf60962822/GCF_014645535.1_ASM1464553v1_genomic.fna.gz | prodigal -d GCF_014645535.1_ASM1464553v1_genomic.fna/cds.fna -a GCF_014645535.1_ASM1464553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:24,501] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:24,501] [INFO] Task started: HMMsearch
[2024-01-24 12:37:24,502] [INFO] Running command: hmmsearch --tblout GCF_014645535.1_ASM1464553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference/reference_markers.hmm GCF_014645535.1_ASM1464553v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:24,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:24,802] [INFO] Found 6/6 markers.
[2024-01-24 12:37:24,850] [INFO] Query marker FASTA was written to GCF_014645535.1_ASM1464553v1_genomic.fna/markers.fasta
[2024-01-24 12:37:24,850] [INFO] Task started: Blastn
[2024-01-24 12:37:24,851] [INFO] Running command: blastn -query GCF_014645535.1_ASM1464553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference/reference_markers.fasta -out GCF_014645535.1_ASM1464553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:25,666] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:25,670] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:25,670] [INFO] Target genome list was writen to GCF_014645535.1_ASM1464553v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:25,681] [INFO] Task started: fastANI
[2024-01-24 12:37:25,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg785b4663-434c-45bc-b5c9-abbf60962822/GCF_014645535.1_ASM1464553v1_genomic.fna.gz --refList GCF_014645535.1_ASM1464553v1_genomic.fna/target_genomes.txt --output GCF_014645535.1_ASM1464553v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:40,863] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:40,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:40,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:40,876] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:40,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:40,877] [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
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	100.0	1522	1523	95	conclusive
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	86.4337	1297	1523	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	85.3174	1258	1523	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	78.8157	413	1523	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	78.4419	406	1523	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.3193	401	1523	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	78.1808	350	1523	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	77.8927	319	1523	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	77.8743	269	1523	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	77.6943	286	1523	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	76.3858	114	1523	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	76.2913	124	1523	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.0589	189	1523	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	75.9238	72	1523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:40,878] [INFO] DFAST Taxonomy check result was written to GCF_014645535.1_ASM1464553v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:40,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:40,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:40,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference/checkm_data
[2024-01-24 12:37:40,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:40,928] [INFO] Task started: CheckM
[2024-01-24 12:37:40,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645535.1_ASM1464553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645535.1_ASM1464553v1_genomic.fna/checkm_input GCF_014645535.1_ASM1464553v1_genomic.fna/checkm_result
[2024-01-24 12:38:28,435] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:28,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:28,454] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:28,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:28,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645535.1_ASM1464553v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:28,455] [INFO] Task started: Blastn
[2024-01-24 12:38:28,455] [INFO] Running command: blastn -query GCF_014645535.1_ASM1464553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4c92c7c-d13f-4dde-bcfc-03489bb20427/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645535.1_ASM1464553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:29,912] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:29,915] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:29,916] [INFO] Target genome list was writen to GCF_014645535.1_ASM1464553v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:29,926] [INFO] Task started: fastANI
[2024-01-24 12:38:29,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg785b4663-434c-45bc-b5c9-abbf60962822/GCF_014645535.1_ASM1464553v1_genomic.fna.gz --refList GCF_014645535.1_ASM1464553v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645535.1_ASM1464553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:42,077] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:42,092] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:42,092] [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_014645535.1	s__Silvimonas iriomotensis	100.0	1522	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014645555.1	s__Silvimonas amylolytica	86.4427	1296	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202765.1	s__Silvimonas terrae	85.3131	1259	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294205.1	s__Amantichitinum ursilacus	79.5658	655	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001313065.1	s__Amantichitinum sp001313065	79.4694	554	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Amantichitinum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	78.8109	414	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	78.4844	411	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	78.4512	405	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	78.3393	399	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808185.1	s__Jeongeupia sp001808185	78.2244	331	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	78.1612	352	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	77.8819	320	1523	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:42,094] [INFO] GTDB search result was written to GCF_014645535.1_ASM1464553v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:42,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:42,098] [INFO] DFAST_QC result json was written to GCF_014645535.1_ASM1464553v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:42,098] [INFO] DFAST_QC completed!
[2024-01-24 12:38:42,098] [INFO] Total running time: 0h1m35s