[2024-01-25 18:46:50,825] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:50,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:50,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference
[2024-01-25 18:46:51,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:51,996] [INFO] Task started: Prodigal
[2024-01-25 18:46:51,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg882c0bba-dbbf-4637-b77b-a613b256ac15/GCF_014647555.1_ASM1464755v1_genomic.fna.gz | prodigal -d GCF_014647555.1_ASM1464755v1_genomic.fna/cds.fna -a GCF_014647555.1_ASM1464755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:00,832] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:00,833] [INFO] Task started: HMMsearch
[2024-01-25 18:47:00,833] [INFO] Running command: hmmsearch --tblout GCF_014647555.1_ASM1464755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference/reference_markers.hmm GCF_014647555.1_ASM1464755v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:01,099] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:01,100] [INFO] Found 6/6 markers.
[2024-01-25 18:47:01,137] [INFO] Query marker FASTA was written to GCF_014647555.1_ASM1464755v1_genomic.fna/markers.fasta
[2024-01-25 18:47:01,137] [INFO] Task started: Blastn
[2024-01-25 18:47:01,137] [INFO] Running command: blastn -query GCF_014647555.1_ASM1464755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference/reference_markers.fasta -out GCF_014647555.1_ASM1464755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:01,806] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:01,808] [INFO] Selected 11 target genomes.
[2024-01-25 18:47:01,809] [INFO] Target genome list was writen to GCF_014647555.1_ASM1464755v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:01,819] [INFO] Task started: fastANI
[2024-01-25 18:47:01,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg882c0bba-dbbf-4637-b77b-a613b256ac15/GCF_014647555.1_ASM1464755v1_genomic.fna.gz --refList GCF_014647555.1_ASM1464755v1_genomic.fna/target_genomes.txt --output GCF_014647555.1_ASM1464755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:13,612] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:13,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:13,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:13,620] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:47:13,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:13,621] [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 putrefaciens	strain=JCM 20190	GCA_014647555.1	24	24	type	True	100.0	1437	1445	95	conclusive
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	99.959	1431	1445	95	conclusive
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	99.924	1387	1445	95	conclusive
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	89.6815	1200	1445	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	86.5451	1130	1445	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	84.8685	1069	1445	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	84.8442	1114	1445	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	82.4882	889	1445	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	81.9896	923	1445	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.6686	903	1445	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.3501	906	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:13,622] [INFO] DFAST Taxonomy check result was written to GCF_014647555.1_ASM1464755v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:13,623] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:13,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:13,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference/checkm_data
[2024-01-25 18:47:13,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:13,667] [INFO] Task started: CheckM
[2024-01-25 18:47:13,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647555.1_ASM1464755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647555.1_ASM1464755v1_genomic.fna/checkm_input GCF_014647555.1_ASM1464755v1_genomic.fna/checkm_result
[2024-01-25 18:47:43,516] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:43,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:43,536] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:43,536] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:43,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647555.1_ASM1464755v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:43,536] [INFO] Task started: Blastn
[2024-01-25 18:47:43,536] [INFO] Running command: blastn -query GCF_014647555.1_ASM1464755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0b28e6a-8ce7-47ee-9afd-7465c2aecabd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647555.1_ASM1464755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:44,558] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:44,565] [INFO] Selected 11 target genomes.
[2024-01-25 18:47:44,565] [INFO] Target genome list was writen to GCF_014647555.1_ASM1464755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:44,587] [INFO] Task started: fastANI
[2024-01-25 18:47:44,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg882c0bba-dbbf-4637-b77b-a613b256ac15/GCF_014647555.1_ASM1464755v1_genomic.fna.gz --refList GCF_014647555.1_ASM1464755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647555.1_ASM1464755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:56,742] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:56,750] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:56,750] [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_016406325.1	s__Shewanella putrefaciens	99.959	1431	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	conclusive
GCF_002966515.1	s__Shewanella sp002966515	86.4255	1118	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_002838165.1	s__Shewanella sp002838165	84.9525	1100	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_900456975.1	s__Shewanella baltica	84.8425	1114	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_016406305.1	s__Shewanella putrefaciens_C	84.4366	1064	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783505.1	s__Shewanella sp002783505	84.3639	1008	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217915.1	s__Shewanella sp000217915	83.9673	984	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	82.1685	933	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_000146165.2	s__Shewanella oneidensis	81.9675	923	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014647135.1	s__Shewanella xiamenensis	81.8573	935	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_000203935.1	s__Shewanella sp000203935	81.6687	933	1445	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:56,752] [INFO] GTDB search result was written to GCF_014647555.1_ASM1464755v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:56,753] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:56,755] [INFO] DFAST_QC result json was written to GCF_014647555.1_ASM1464755v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:56,755] [INFO] DFAST_QC completed!
[2024-01-25 18:47:56,756] [INFO] Total running time: 0h1m6s