[2024-01-24 12:21:57,506] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference
[2024-01-24 12:21:58,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,978] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,978] [INFO] Running command: gunzip -c /var/lib/cwl/stg92547d72-0ad9-4f31-8046-bed69f793a1d/GCF_000146165.2_ASM14616v2_genomic.fna.gz | prodigal -d GCF_000146165.2_ASM14616v2_genomic.fna/cds.fna -a GCF_000146165.2_ASM14616v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:11,874] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:11,875] [INFO] Task started: HMMsearch
[2024-01-24 12:22:11,875] [INFO] Running command: hmmsearch --tblout GCF_000146165.2_ASM14616v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference/reference_markers.hmm GCF_000146165.2_ASM14616v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:12,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:12,247] [INFO] Found 6/6 markers.
[2024-01-24 12:22:12,288] [INFO] Query marker FASTA was written to GCF_000146165.2_ASM14616v2_genomic.fna/markers.fasta
[2024-01-24 12:22:12,289] [INFO] Task started: Blastn
[2024-01-24 12:22:12,289] [INFO] Running command: blastn -query GCF_000146165.2_ASM14616v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference/reference_markers.fasta -out GCF_000146165.2_ASM14616v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:13,078] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:13,082] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:13,082] [INFO] Target genome list was writen to GCF_000146165.2_ASM14616v2_genomic.fna/target_genomes.txt
[2024-01-24 12:22:13,086] [INFO] Task started: fastANI
[2024-01-24 12:22:13,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg92547d72-0ad9-4f31-8046-bed69f793a1d/GCF_000146165.2_ASM14616v2_genomic.fna.gz --refList GCF_000146165.2_ASM14616v2_genomic.fna/target_genomes.txt --output GCF_000146165.2_ASM14616v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:29,483] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:29,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:29,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:29,493] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:29,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:29,493] [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 oneidensis	strain=MR-1	GCA_000146165.2	70863	70863	type	True	100.0	1709	1709	95	conclusive
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	99.9884	1655	1709	95	conclusive
Shewanella xiamenensis	strain=JCM 16212	GCA_014647135.1	332186	332186	type	True	89.3659	1291	1709	95	below_threshold
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	86.7138	1275	1709	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	86.2945	1214	1709	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	86.0925	1245	1709	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	81.4347	906	1709	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	80.6766	775	1709	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	78.8936	264	1709	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:29,495] [INFO] DFAST Taxonomy check result was written to GCF_000146165.2_ASM14616v2_genomic.fna/tc_result.tsv
[2024-01-24 12:22:29,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:29,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:29,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference/checkm_data
[2024-01-24 12:22:29,497] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:29,546] [INFO] Task started: CheckM
[2024-01-24 12:22:29,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000146165.2_ASM14616v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000146165.2_ASM14616v2_genomic.fna/checkm_input GCF_000146165.2_ASM14616v2_genomic.fna/checkm_result
[2024-01-24 12:23:10,446] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:10,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:10,468] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:10,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:10,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000146165.2_ASM14616v2_genomic.fna/markers.fasta)
[2024-01-24 12:23:10,469] [INFO] Task started: Blastn
[2024-01-24 12:23:10,469] [INFO] Running command: blastn -query GCF_000146165.2_ASM14616v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c4cd931-18ea-4a87-a7cc-8f30b471535a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000146165.2_ASM14616v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:11,596] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:11,599] [INFO] Selected 6 target genomes.
[2024-01-24 12:23:11,599] [INFO] Target genome list was writen to GCF_000146165.2_ASM14616v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:11,604] [INFO] Task started: fastANI
[2024-01-24 12:23:11,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg92547d72-0ad9-4f31-8046-bed69f793a1d/GCF_000146165.2_ASM14616v2_genomic.fna.gz --refList GCF_000146165.2_ASM14616v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000146165.2_ASM14616v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:22,424] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:22,430] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:22,430] [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_000146165.2	s__Shewanella oneidensis	100.0	1709	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_014647135.1	s__Shewanella xiamenensis	89.3785	1289	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_000485795.1	s__Shewanella decolorationis	86.7298	1273	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_000014665.1	s__Shewanella sp000014665	86.3715	1220	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
GCF_000203935.1	s__Shewanella sp000203935	86.3002	1267	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_002216875.1	s__Shewanella bicestrii	86.2493	1249	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:22,432] [INFO] GTDB search result was written to GCF_000146165.2_ASM14616v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:22,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:22,436] [INFO] DFAST_QC result json was written to GCF_000146165.2_ASM14616v2_genomic.fna/dqc_result.json
[2024-01-24 12:23:22,436] [INFO] DFAST_QC completed!
[2024-01-24 12:23:22,436] [INFO] Total running time: 0h1m25s