[2024-01-24 13:57:32,214] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,216] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference
[2024-01-24 13:57:33,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,577] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg13b398a9-daea-4364-93dd-f01c84211c01/GCF_019655015.1_ASM1965501v1_genomic.fna.gz | prodigal -d GCF_019655015.1_ASM1965501v1_genomic.fna/cds.fna -a GCF_019655015.1_ASM1965501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:44,988] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:44,989] [INFO] Task started: HMMsearch
[2024-01-24 13:57:44,989] [INFO] Running command: hmmsearch --tblout GCF_019655015.1_ASM1965501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference/reference_markers.hmm GCF_019655015.1_ASM1965501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:45,387] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:45,388] [INFO] Found 6/6 markers.
[2024-01-24 13:57:45,439] [INFO] Query marker FASTA was written to GCF_019655015.1_ASM1965501v1_genomic.fna/markers.fasta
[2024-01-24 13:57:45,440] [INFO] Task started: Blastn
[2024-01-24 13:57:45,440] [INFO] Running command: blastn -query GCF_019655015.1_ASM1965501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference/reference_markers.fasta -out GCF_019655015.1_ASM1965501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:46,238] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:46,241] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:46,242] [INFO] Target genome list was writen to GCF_019655015.1_ASM1965501v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:46,246] [INFO] Task started: fastANI
[2024-01-24 13:57:46,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b398a9-daea-4364-93dd-f01c84211c01/GCF_019655015.1_ASM1965501v1_genomic.fna.gz --refList GCF_019655015.1_ASM1965501v1_genomic.fna/target_genomes.txt --output GCF_019655015.1_ASM1965501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:57,265] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:57,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:57,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:57,275] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:57,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:57,275] [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
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	100.0	1662	1668	95	conclusive
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	99.9536	1612	1668	95	conclusive
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	88.2343	1196	1668	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	83.1814	1030	1668	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	82.6846	979	1668	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	82.172	875	1668	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	82.1682	887	1668	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	79.8591	571	1668	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.6748	569	1668	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	78.7832	323	1668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:57,279] [INFO] DFAST Taxonomy check result was written to GCF_019655015.1_ASM1965501v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:57,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:57,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:57,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference/checkm_data
[2024-01-24 13:57:57,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:57,335] [INFO] Task started: CheckM
[2024-01-24 13:57:57,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019655015.1_ASM1965501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019655015.1_ASM1965501v1_genomic.fna/checkm_input GCF_019655015.1_ASM1965501v1_genomic.fna/checkm_result
[2024-01-24 13:58:33,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:33,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,992] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:33,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:33,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019655015.1_ASM1965501v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:33,993] [INFO] Task started: Blastn
[2024-01-24 13:58:33,993] [INFO] Running command: blastn -query GCF_019655015.1_ASM1965501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01a8e0e8-aef6-4484-b315-8f213e57455b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019655015.1_ASM1965501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:35,129] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:35,132] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:35,132] [INFO] Target genome list was writen to GCF_019655015.1_ASM1965501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:35,150] [INFO] Task started: fastANI
[2024-01-24 13:58:35,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg13b398a9-daea-4364-93dd-f01c84211c01/GCF_019655015.1_ASM1965501v1_genomic.fna.gz --refList GCF_019655015.1_ASM1965501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019655015.1_ASM1965501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:47,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:47,712] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:47,712] [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_000518605.1	s__Shewanella fidelis	83.1773	1032	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_000018285.1	s__Shewanella pealeana	82.6822	979	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	82.277	907	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	82.1812	887	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	80.2589	619	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	79.9586	581	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836205.1	s__Shewanella sp002836205	79.8843	585	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.46	99.13	0.96	0.92	4	-
GCF_003605125.1	s__Shewanella algidipiscicola	78.7949	320	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_001957125.1	s__Shewanella sp001957125	78.7404	384	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018025.1	s__Shewanella sediminis	78.6641	344	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	78.0836	272	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	77.9517	259	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,714] [INFO] GTDB search result was written to GCF_019655015.1_ASM1965501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:47,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:47,717] [INFO] DFAST_QC result json was written to GCF_019655015.1_ASM1965501v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:47,717] [INFO] DFAST_QC completed!
[2024-01-24 13:58:47,718] [INFO] Total running time: 0h1m16s