[2024-01-24 11:20:34,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference
[2024-01-24 11:20:35,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,630] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg41eb2fa2-350c-42a2-bb1d-4e69ec74bfb5/GCF_019457475.1_ASM1945747v1_genomic.fna.gz | prodigal -d GCF_019457475.1_ASM1945747v1_genomic.fna/cds.fna -a GCF_019457475.1_ASM1945747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:46,335] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:46,336] [INFO] Task started: HMMsearch
[2024-01-24 11:20:46,336] [INFO] Running command: hmmsearch --tblout GCF_019457475.1_ASM1945747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference/reference_markers.hmm GCF_019457475.1_ASM1945747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:46,584] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:46,586] [INFO] Found 6/6 markers.
[2024-01-24 11:20:46,623] [INFO] Query marker FASTA was written to GCF_019457475.1_ASM1945747v1_genomic.fna/markers.fasta
[2024-01-24 11:20:46,623] [INFO] Task started: Blastn
[2024-01-24 11:20:46,623] [INFO] Running command: blastn -query GCF_019457475.1_ASM1945747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference/reference_markers.fasta -out GCF_019457475.1_ASM1945747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:47,406] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:47,410] [INFO] Selected 10 target genomes.
[2024-01-24 11:20:47,411] [INFO] Target genome list was writen to GCF_019457475.1_ASM1945747v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:47,417] [INFO] Task started: fastANI
[2024-01-24 11:20:47,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg41eb2fa2-350c-42a2-bb1d-4e69ec74bfb5/GCF_019457475.1_ASM1945747v1_genomic.fna.gz --refList GCF_019457475.1_ASM1945747v1_genomic.fna/target_genomes.txt --output GCF_019457475.1_ASM1945747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:56,184] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:56,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:56,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:56,198] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:56,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:56,198] [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 seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	82.0582	855	1377	95	below_threshold
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	82.0063	830	1377	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	81.8251	771	1377	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_000146165.2	70863	70863	type	True	81.782	763	1377	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.7786	895	1377	95	below_threshold
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	81.6525	789	1377	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	80.4192	651	1377	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	80.4117	684	1377	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	78.1088	255	1377	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	77.8595	269	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:56,199] [INFO] DFAST Taxonomy check result was written to GCF_019457475.1_ASM1945747v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:56,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:56,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:56,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference/checkm_data
[2024-01-24 11:20:56,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:56,239] [INFO] Task started: CheckM
[2024-01-24 11:20:56,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457475.1_ASM1945747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457475.1_ASM1945747v1_genomic.fna/checkm_input GCF_019457475.1_ASM1945747v1_genomic.fna/checkm_result
[2024-01-24 11:21:32,319] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:32,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:32,337] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:32,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:32,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457475.1_ASM1945747v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:32,338] [INFO] Task started: Blastn
[2024-01-24 11:21:32,339] [INFO] Running command: blastn -query GCF_019457475.1_ASM1945747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd21e32f0-4225-48c2-a9b2-ea54d1c8c6b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457475.1_ASM1945747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:33,530] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:33,533] [INFO] Selected 7 target genomes.
[2024-01-24 11:21:33,534] [INFO] Target genome list was writen to GCF_019457475.1_ASM1945747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:33,543] [INFO] Task started: fastANI
[2024-01-24 11:21:33,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg41eb2fa2-350c-42a2-bb1d-4e69ec74bfb5/GCF_019457475.1_ASM1945747v1_genomic.fna.gz --refList GCF_019457475.1_ASM1945747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457475.1_ASM1945747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:40,971] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:40,977] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:40,978] [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_002216875.1	s__Shewanella bicestrii	82.2596	876	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_000203935.1	s__Shewanella sp000203935	82.2307	884	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_000014665.1	s__Shewanella sp000014665	82.1078	878	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
GCF_000485795.1	s__Shewanella decolorationis	82.0258	827	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_000146165.2	s__Shewanella oneidensis	81.8364	760	1377	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	81.6629	790	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_016406305.1	s__Shewanella putrefaciens_C	81.0996	754	1377	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 11:21:40,979] [INFO] GTDB search result was written to GCF_019457475.1_ASM1945747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:40,980] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:40,984] [INFO] DFAST_QC result json was written to GCF_019457475.1_ASM1945747v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:40,984] [INFO] DFAST_QC completed!
[2024-01-24 11:21:40,984] [INFO] Total running time: 0h1m7s