[2024-01-24 11:51:19,540] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference
[2024-01-24 11:51:20,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:20,756] [INFO] Task started: Prodigal
[2024-01-24 11:51:20,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg41418b26-4074-4719-863f-61a1f45c6568/GCF_023283845.1_ASM2328384v1_genomic.fna.gz | prodigal -d GCF_023283845.1_ASM2328384v1_genomic.fna/cds.fna -a GCF_023283845.1_ASM2328384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:30,890] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:30,890] [INFO] Task started: HMMsearch
[2024-01-24 11:51:30,890] [INFO] Running command: hmmsearch --tblout GCF_023283845.1_ASM2328384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference/reference_markers.hmm GCF_023283845.1_ASM2328384v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:31,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:31,193] [INFO] Found 6/6 markers.
[2024-01-24 11:51:31,237] [INFO] Query marker FASTA was written to GCF_023283845.1_ASM2328384v1_genomic.fna/markers.fasta
[2024-01-24 11:51:31,237] [INFO] Task started: Blastn
[2024-01-24 11:51:31,237] [INFO] Running command: blastn -query GCF_023283845.1_ASM2328384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference/reference_markers.fasta -out GCF_023283845.1_ASM2328384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:32,008] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:32,013] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:32,013] [INFO] Target genome list was writen to GCF_023283845.1_ASM2328384v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:32,033] [INFO] Task started: fastANI
[2024-01-24 11:51:32,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg41418b26-4074-4719-863f-61a1f45c6568/GCF_023283845.1_ASM2328384v1_genomic.fna.gz --refList GCF_023283845.1_ASM2328384v1_genomic.fna/target_genomes.txt --output GCF_023283845.1_ASM2328384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:42,683] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:42,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:42,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:42,696] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:42,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:42,696] [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 marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	100.0	1597	1599	95	conclusive
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	88.0402	1201	1599	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	88.0205	1205	1599	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	82.8296	990	1599	95	below_threshold
Shewanella fidelis	strain=ATCC BAA-318	GCA_000518605.1	173509	173509	type	True	82.6078	1061	1599	95	below_threshold
Shewanella halifaxensis	strain=HAW-EB4	GCA_000019185.1	271098	271098	type	True	82.1076	972	1599	95	below_threshold
Shewanella schlegeliana	strain=JCM 11561	GCA_016765635.1	190308	190308	type	True	82.1066	944	1599	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	81.9799	961	1599	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	79.6392	612	1599	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.5954	604	1599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:42,699] [INFO] DFAST Taxonomy check result was written to GCF_023283845.1_ASM2328384v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:42,699] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:42,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:42,700] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference/checkm_data
[2024-01-24 11:51:42,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:42,751] [INFO] Task started: CheckM
[2024-01-24 11:51:42,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023283845.1_ASM2328384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023283845.1_ASM2328384v1_genomic.fna/checkm_input GCF_023283845.1_ASM2328384v1_genomic.fna/checkm_result
[2024-01-24 11:52:17,307] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:17,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:17,332] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:17,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:17,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023283845.1_ASM2328384v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:17,333] [INFO] Task started: Blastn
[2024-01-24 11:52:17,334] [INFO] Running command: blastn -query GCF_023283845.1_ASM2328384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d3ddde8-00dd-4f76-b5ed-4c31df9012cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_023283845.1_ASM2328384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:18,534] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:18,538] [INFO] Selected 9 target genomes.
[2024-01-24 11:52:18,539] [INFO] Target genome list was writen to GCF_023283845.1_ASM2328384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:18,546] [INFO] Task started: fastANI
[2024-01-24 11:52:18,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg41418b26-4074-4719-863f-61a1f45c6568/GCF_023283845.1_ASM2328384v1_genomic.fna.gz --refList GCF_023283845.1_ASM2328384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023283845.1_ASM2328384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:27,451] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:27,463] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:27,464] [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_000018285.1	s__Shewanella pealeana	82.8314	991	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	82.6033	1063	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
GCF_016765635.1	s__Shewanella schlegeliana	82.1183	945	1599	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	82.0947	975	1599	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	80.0397	653	1599	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	79.6822	631	1599	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	79.6143	653	1599	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	78.6409	321	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_007567505.1	s__Shewanella donghaensis	77.7816	305	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:27,465] [INFO] GTDB search result was written to GCF_023283845.1_ASM2328384v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:27,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:27,469] [INFO] DFAST_QC result json was written to GCF_023283845.1_ASM2328384v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:27,469] [INFO] DFAST_QC completed!
[2024-01-24 11:52:27,469] [INFO] Total running time: 0h1m8s