[2024-01-25 19:24:45,019] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference
[2024-01-25 19:24:48,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,242] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,242] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc2d94ef-85b8-4a3c-b578-fd60eecc4c49/GCF_015069875.1_ASM1506987v1_genomic.fna.gz | prodigal -d GCF_015069875.1_ASM1506987v1_genomic.fna/cds.fna -a GCF_015069875.1_ASM1506987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:56,112] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:56,113] [INFO] Task started: HMMsearch
[2024-01-25 19:24:56,113] [INFO] Running command: hmmsearch --tblout GCF_015069875.1_ASM1506987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference/reference_markers.hmm GCF_015069875.1_ASM1506987v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:56,323] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:56,324] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfc2d94ef-85b8-4a3c-b578-fd60eecc4c49/GCF_015069875.1_ASM1506987v1_genomic.fna.gz]
[2024-01-25 19:24:56,353] [INFO] Query marker FASTA was written to GCF_015069875.1_ASM1506987v1_genomic.fna/markers.fasta
[2024-01-25 19:24:56,354] [INFO] Task started: Blastn
[2024-01-25 19:24:56,354] [INFO] Running command: blastn -query GCF_015069875.1_ASM1506987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference/reference_markers.fasta -out GCF_015069875.1_ASM1506987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:24:57,056] [INFO] Task succeeded: Blastn
[2024-01-25 19:24:57,062] [INFO] Selected 11 target genomes.
[2024-01-25 19:24:57,063] [INFO] Target genome list was writen to GCF_015069875.1_ASM1506987v1_genomic.fna/target_genomes.txt
[2024-01-25 19:24:57,192] [INFO] Task started: fastANI
[2024-01-25 19:24:57,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc2d94ef-85b8-4a3c-b578-fd60eecc4c49/GCF_015069875.1_ASM1506987v1_genomic.fna.gz --refList GCF_015069875.1_ASM1506987v1_genomic.fna/target_genomes.txt --output GCF_015069875.1_ASM1506987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:08,444] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:08,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:08,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:08,452] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:25:08,452] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:08,452] [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 benthica	strain=DSM 8812	GCA_015069875.1	43661	43661	type	True	100.0	1321	1321	95	conclusive
Shewanella psychropiezotolerans	strain=YLB-06	GCA_007197555.1	2593655	2593655	type	True	92.0712	1078	1321	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	86.6932	922	1321	95	below_threshold
Shewanella psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	86.4208	1035	1321	95	below_threshold
Shewanella eurypsychrophilus	strain=YLB-08	GCA_007004545.3	2593656	2593656	type	True	82.6407	815	1321	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	78.0878	274	1321	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	77.3681	166	1321	95	below_threshold
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	77.2431	145	1321	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	77.1519	120	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:08,453] [INFO] DFAST Taxonomy check result was written to GCF_015069875.1_ASM1506987v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:08,454] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:08,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:08,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference/checkm_data
[2024-01-25 19:25:08,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:08,495] [INFO] Task started: CheckM
[2024-01-25 19:25:08,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015069875.1_ASM1506987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015069875.1_ASM1506987v1_genomic.fna/checkm_input GCF_015069875.1_ASM1506987v1_genomic.fna/checkm_result
[2024-01-25 19:25:36,978] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:36,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:37,000] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:37,000] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:37,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015069875.1_ASM1506987v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:37,000] [INFO] Task started: Blastn
[2024-01-25 19:25:37,001] [INFO] Running command: blastn -query GCF_015069875.1_ASM1506987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67f87501-cbc2-4757-8151-178b3ab62138/dqc_reference/reference_markers_gtdb.fasta -out GCF_015069875.1_ASM1506987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:38,134] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:38,140] [INFO] Selected 7 target genomes.
[2024-01-25 19:25:38,140] [INFO] Target genome list was writen to GCF_015069875.1_ASM1506987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:38,147] [INFO] Task started: fastANI
[2024-01-25 19:25:38,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc2d94ef-85b8-4a3c-b578-fd60eecc4c49/GCF_015069875.1_ASM1506987v1_genomic.fna.gz --refList GCF_015069875.1_ASM1506987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015069875.1_ASM1506987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:25:47,188] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:47,193] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:25:47,194] [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_015069875.1	s__Shewanella benthica	100.0	1321	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	conclusive
GCF_000172075.1	s__Shewanella benthica_A	93.687	900	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.25	96.25	0.86	0.86	2	-
GCF_007197555.1	s__Shewanella sp007197555	92.06	1079	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.43	99.43	0.94	0.94	2	-
GCA_013214165.1	s__Shewanella sp013214165	90.8421	862	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091325.1	s__Shewanella violacea	86.7037	921	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005305.1	s__Shewanella psychrophila	86.405	1037	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004545.2	s__Shewanella sp007004545	82.6004	808	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:25:47,195] [INFO] GTDB search result was written to GCF_015069875.1_ASM1506987v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:25:47,195] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:25:47,198] [INFO] DFAST_QC result json was written to GCF_015069875.1_ASM1506987v1_genomic.fna/dqc_result.json
[2024-01-25 19:25:47,198] [INFO] DFAST_QC completed!
[2024-01-25 19:25:47,198] [INFO] Total running time: 0h1m2s