[2024-01-25 18:10:50,503] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:50,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:50,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference
[2024-01-25 18:10:51,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:51,705] [INFO] Task started: Prodigal
[2024-01-25 18:10:51,705] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa8be6c9-7a44-4ed0-bfd7-4969e6ed0e4f/GCF_000291685.1_ASM29168v1_genomic.fna.gz | prodigal -d GCF_000291685.1_ASM29168v1_genomic.fna/cds.fna -a GCF_000291685.1_ASM29168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:00,017] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:00,018] [INFO] Task started: HMMsearch
[2024-01-25 18:11:00,018] [INFO] Running command: hmmsearch --tblout GCF_000291685.1_ASM29168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference/reference_markers.hmm GCF_000291685.1_ASM29168v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:00,263] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:00,264] [INFO] Found 6/6 markers.
[2024-01-25 18:11:00,300] [INFO] Query marker FASTA was written to GCF_000291685.1_ASM29168v1_genomic.fna/markers.fasta
[2024-01-25 18:11:00,300] [INFO] Task started: Blastn
[2024-01-25 18:11:00,301] [INFO] Running command: blastn -query GCF_000291685.1_ASM29168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference/reference_markers.fasta -out GCF_000291685.1_ASM29168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:00,969] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:00,972] [INFO] Selected 10 target genomes.
[2024-01-25 18:11:00,973] [INFO] Target genome list was writen to GCF_000291685.1_ASM29168v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:00,986] [INFO] Task started: fastANI
[2024-01-25 18:11:00,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8be6c9-7a44-4ed0-bfd7-4969e6ed0e4f/GCF_000291685.1_ASM29168v1_genomic.fna.gz --refList GCF_000291685.1_ASM29168v1_genomic.fna/target_genomes.txt --output GCF_000291685.1_ASM29168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:10,386] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:10,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:10,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:10,394] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:11:10,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:10,394] [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
Moritella marina	strain=ATCC 15381	GCA_000291685.1	90736	90736	type	True	100.0	1510	1512	95	conclusive
Moritella marina	strain=MP-1	GCA_000381865.1	90736	90736	type	True	99.9961	1502	1512	95	conclusive
Moritella marina	strain=MP-1	GCA_008931805.1	90736	90736	type	True	99.9944	1509	1512	95	conclusive
Moritella dasanensis	strain=ArB 0140	GCA_000276805.1	428031	428031	type	True	87.1888	1196	1512	95	below_threshold
Moritella yayanosii	strain=DB21MT 5	GCA_900465055.1	69539	69539	type	True	83.5032	952	1512	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	77.0463	121	1512	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	76.9519	81	1512	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	76.6732	113	1512	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	76.6536	92	1512	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	76.1484	63	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:10,396] [INFO] DFAST Taxonomy check result was written to GCF_000291685.1_ASM29168v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:10,396] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:10,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:10,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference/checkm_data
[2024-01-25 18:11:10,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:10,442] [INFO] Task started: CheckM
[2024-01-25 18:11:10,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000291685.1_ASM29168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000291685.1_ASM29168v1_genomic.fna/checkm_input GCF_000291685.1_ASM29168v1_genomic.fna/checkm_result
[2024-01-25 18:11:39,154] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:39,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:39,175] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:39,175] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:39,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000291685.1_ASM29168v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:39,176] [INFO] Task started: Blastn
[2024-01-25 18:11:39,176] [INFO] Running command: blastn -query GCF_000291685.1_ASM29168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a51b9c7-193e-4b8a-8c86-31f47a371236/dqc_reference/reference_markers_gtdb.fasta -out GCF_000291685.1_ASM29168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:40,250] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:40,256] [INFO] Selected 8 target genomes.
[2024-01-25 18:11:40,256] [INFO] Target genome list was writen to GCF_000291685.1_ASM29168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:40,266] [INFO] Task started: fastANI
[2024-01-25 18:11:40,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8be6c9-7a44-4ed0-bfd7-4969e6ed0e4f/GCF_000291685.1_ASM29168v1_genomic.fna.gz --refList GCF_000291685.1_ASM29168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000291685.1_ASM29168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:49,675] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:49,682] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:49,682] [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_008931805.1	s__Moritella marina	99.9944	1509	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_015082335.1	s__Moritella sp015082335	90.6285	1294	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000276805.1	s__Moritella dasanensis	87.2004	1194	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836355.1	s__Moritella sp002836355	86.8817	1193	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170855.1	s__Moritella sp000170855	83.8794	1073	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	97.45	95.37	0.88	0.83	4	-
GCF_018219155.1	s__Moritella sp018219155	83.8538	1020	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000953735.1	s__Moritella viscosa	83.514	980	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	99.48	99.13	0.93	0.91	13	-
GCF_018219455.1	s__Moritella sp018219455	83.468	1021	1512	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	96.81	96.78	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:49,684] [INFO] GTDB search result was written to GCF_000291685.1_ASM29168v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:49,685] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:49,688] [INFO] DFAST_QC result json was written to GCF_000291685.1_ASM29168v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:49,688] [INFO] DFAST_QC completed!
[2024-01-25 18:11:49,689] [INFO] Total running time: 0h0m59s