[2024-01-24 12:06:33,877] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,879] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference
[2024-01-24 12:06:35,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,105] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6b4a4ec-f18b-4e74-95f7-226910d643c2/GCF_003254175.1_ASM325417v1_genomic.fna.gz | prodigal -d GCF_003254175.1_ASM325417v1_genomic.fna/cds.fna -a GCF_003254175.1_ASM325417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:47,330] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:47,331] [INFO] Task started: HMMsearch
[2024-01-24 12:06:47,331] [INFO] Running command: hmmsearch --tblout GCF_003254175.1_ASM325417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference/reference_markers.hmm GCF_003254175.1_ASM325417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:47,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:47,584] [INFO] Found 6/6 markers.
[2024-01-24 12:06:47,624] [INFO] Query marker FASTA was written to GCF_003254175.1_ASM325417v1_genomic.fna/markers.fasta
[2024-01-24 12:06:47,624] [INFO] Task started: Blastn
[2024-01-24 12:06:47,624] [INFO] Running command: blastn -query GCF_003254175.1_ASM325417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference/reference_markers.fasta -out GCF_003254175.1_ASM325417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:48,349] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:48,353] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:48,353] [INFO] Target genome list was writen to GCF_003254175.1_ASM325417v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:48,358] [INFO] Task started: fastANI
[2024-01-24 12:06:48,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b4a4ec-f18b-4e74-95f7-226910d643c2/GCF_003254175.1_ASM325417v1_genomic.fna.gz --refList GCF_003254175.1_ASM325417v1_genomic.fna/target_genomes.txt --output GCF_003254175.1_ASM325417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:57,092] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:57,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:57,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:57,104] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:06:57,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:57,104] [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
Celeribacter halophilus	strain=DSM 26270	GCA_003254175.1	576117	576117	type	True	100.0	1260	1262	95	conclusive
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	99.9881	1254	1262	95	conclusive
Celeribacter halophilus	strain=CGMCC 1.8891	GCA_900114135.1	576117	576117	type	True	99.9785	1249	1262	95	conclusive
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	81.0765	688	1262	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	80.849	695	1262	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	80.7098	673	1262	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	79.3962	483	1262	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.3229	206	1262	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.9938	210	1262	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.8121	185	1262	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7393	192	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:57,106] [INFO] DFAST Taxonomy check result was written to GCF_003254175.1_ASM325417v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:57,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:57,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:57,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference/checkm_data
[2024-01-24 12:06:57,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:57,145] [INFO] Task started: CheckM
[2024-01-24 12:06:57,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254175.1_ASM325417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254175.1_ASM325417v1_genomic.fna/checkm_input GCF_003254175.1_ASM325417v1_genomic.fna/checkm_result
[2024-01-24 12:07:36,181] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:36,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,208] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:36,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:36,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254175.1_ASM325417v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:36,209] [INFO] Task started: Blastn
[2024-01-24 12:07:36,209] [INFO] Running command: blastn -query GCF_003254175.1_ASM325417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b62980e-9508-4737-9eb8-bd51904e71d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254175.1_ASM325417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:37,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:37,245] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:37,245] [INFO] Target genome list was writen to GCF_003254175.1_ASM325417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:37,255] [INFO] Task started: fastANI
[2024-01-24 12:07:37,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b4a4ec-f18b-4e74-95f7-226910d643c2/GCF_003254175.1_ASM325417v1_genomic.fna.gz --refList GCF_003254175.1_ASM325417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254175.1_ASM325417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:43,548] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:43,560] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:43,560] [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_900114135.1	s__Celeribacter halophilus	99.9785	1249	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	conclusive
GCF_011806455.1	s__Celeribacter sp011806455	81.9119	733	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_001550095.1	s__Celeribacter ethanolicus	81.0834	689	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900113955.1	s__Celeribacter neptunius	80.8581	694	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050785.1	s__Celeribacter persicus	80.7249	671	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299875.1	s__Celeribacter baekdonensis_A	78.9975	556	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	99.07	99.01	0.95	0.93	3	-
GCF_001308265.1	s__Celeribacter_A marinus	78.0137	264	1262	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter_A	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:43,562] [INFO] GTDB search result was written to GCF_003254175.1_ASM325417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:43,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:43,565] [INFO] DFAST_QC result json was written to GCF_003254175.1_ASM325417v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:43,566] [INFO] DFAST_QC completed!
[2024-01-24 12:07:43,566] [INFO] Total running time: 0h1m10s