[2024-01-24 13:41:25,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,363] [INFO] DQC Reference Directory: /var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference
[2024-01-24 13:41:26,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:26,593] [INFO] Task started: Prodigal
[2024-01-24 13:41:26,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg99e6ec0e-582d-4358-b7ea-705267d9a32b/GCF_019655335.1_ASM1965533v1_genomic.fna.gz | prodigal -d GCF_019655335.1_ASM1965533v1_genomic.fna/cds.fna -a GCF_019655335.1_ASM1965533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:38,095] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:38,095] [INFO] Task started: HMMsearch
[2024-01-24 13:41:38,095] [INFO] Running command: hmmsearch --tblout GCF_019655335.1_ASM1965533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference/reference_markers.hmm GCF_019655335.1_ASM1965533v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:38,436] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:38,437] [INFO] Found 6/6 markers.
[2024-01-24 13:41:38,478] [INFO] Query marker FASTA was written to GCF_019655335.1_ASM1965533v1_genomic.fna/markers.fasta
[2024-01-24 13:41:38,478] [INFO] Task started: Blastn
[2024-01-24 13:41:38,478] [INFO] Running command: blastn -query GCF_019655335.1_ASM1965533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference/reference_markers.fasta -out GCF_019655335.1_ASM1965533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:39,291] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:39,294] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:39,295] [INFO] Target genome list was writen to GCF_019655335.1_ASM1965533v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:39,303] [INFO] Task started: fastANI
[2024-01-24 13:41:39,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e6ec0e-582d-4358-b7ea-705267d9a32b/GCF_019655335.1_ASM1965533v1_genomic.fna.gz --refList GCF_019655335.1_ASM1965533v1_genomic.fna/target_genomes.txt --output GCF_019655335.1_ASM1965533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:52,371] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:52,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:52,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:52,381] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:52,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:52,382] [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 hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	100.0	1529	1542	95	conclusive
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	94.4014	1366	1542	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	91.6072	1317	1542	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	85.2953	952	1542	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	85.159	1071	1542	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	84.9419	1067	1542	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	84.8884	1075	1542	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	84.8155	1041	1542	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	84.707	1047	1542	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.8813	971	1542	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.6245	978	1542	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:52,384] [INFO] DFAST Taxonomy check result was written to GCF_019655335.1_ASM1965533v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:52,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:52,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:52,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference/checkm_data
[2024-01-24 13:41:52,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:52,437] [INFO] Task started: CheckM
[2024-01-24 13:41:52,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019655335.1_ASM1965533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019655335.1_ASM1965533v1_genomic.fna/checkm_input GCF_019655335.1_ASM1965533v1_genomic.fna/checkm_result
[2024-01-24 13:42:30,252] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:30,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:30,276] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:30,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:30,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019655335.1_ASM1965533v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:30,278] [INFO] Task started: Blastn
[2024-01-24 13:42:30,278] [INFO] Running command: blastn -query GCF_019655335.1_ASM1965533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge12b519b-f95e-42c6-95a9-ae38d7fee0c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019655335.1_ASM1965533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:31,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:31,423] [INFO] Selected 8 target genomes.
[2024-01-24 13:42:31,423] [INFO] Target genome list was writen to GCF_019655335.1_ASM1965533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:31,464] [INFO] Task started: fastANI
[2024-01-24 13:42:31,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg99e6ec0e-582d-4358-b7ea-705267d9a32b/GCF_019655335.1_ASM1965533v1_genomic.fna.gz --refList GCF_019655335.1_ASM1965533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019655335.1_ASM1965533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:41,396] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:41,411] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:41,411] [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_002838165.1	s__Shewanella sp002838165	97.4369	1431	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	conclusive
GCF_900456975.1	s__Shewanella baltica	94.3888	1367	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_002966515.1	s__Shewanella sp002966515	91.5337	1334	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCA_002783505.1	s__Shewanella sp002783505	85.93	1105	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406305.1	s__Shewanella putrefaciens_C	84.9661	1112	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406325.1	s__Shewanella putrefaciens	84.9435	1067	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_900156405.1	s__Shewanella morhuae	84.8827	1076	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_000014665.1	s__Shewanella sp000014665	81.862	979	1542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,413] [INFO] GTDB search result was written to GCF_019655335.1_ASM1965533v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:41,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:41,417] [INFO] DFAST_QC result json was written to GCF_019655335.1_ASM1965533v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:41,417] [INFO] DFAST_QC completed!
[2024-01-24 13:42:41,417] [INFO] Total running time: 0h1m16s