[2024-01-24 12:40:20,654] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference
[2024-01-24 12:40:21,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,867] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgd81b26ac-89c2-4cdf-bdd7-0f7586937f89/GCF_000615005.1_ASM61500v1_genomic.fna.gz | prodigal -d GCF_000615005.1_ASM61500v1_genomic.fna/cds.fna -a GCF_000615005.1_ASM61500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:31,652] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:31,653] [INFO] Task started: HMMsearch
[2024-01-24 12:40:31,653] [INFO] Running command: hmmsearch --tblout GCF_000615005.1_ASM61500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference/reference_markers.hmm GCF_000615005.1_ASM61500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:31,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:31,937] [INFO] Found 6/6 markers.
[2024-01-24 12:40:31,973] [INFO] Query marker FASTA was written to GCF_000615005.1_ASM61500v1_genomic.fna/markers.fasta
[2024-01-24 12:40:31,974] [INFO] Task started: Blastn
[2024-01-24 12:40:31,974] [INFO] Running command: blastn -query GCF_000615005.1_ASM61500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference/reference_markers.fasta -out GCF_000615005.1_ASM61500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:32,705] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:32,709] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:32,709] [INFO] Target genome list was writen to GCF_000615005.1_ASM61500v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:32,714] [INFO] Task started: fastANI
[2024-01-24 12:40:32,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgd81b26ac-89c2-4cdf-bdd7-0f7586937f89/GCF_000615005.1_ASM61500v1_genomic.fna.gz --refList GCF_000615005.1_ASM61500v1_genomic.fna/target_genomes.txt --output GCF_000615005.1_ASM61500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:45,380] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:45,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:45,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:45,395] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:40:45,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:45,395] [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	99.9718	1412	1415	95	conclusive
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	99.941	1414	1415	95	conclusive
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	99.9033	1372	1415	95	conclusive
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	89.6491	1185	1415	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	86.3746	1121	1415	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	84.91	1043	1415	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	84.762	1079	1415	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	82.5791	877	1415	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	81.9666	891	1415	95	below_threshold
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	81.6751	882	1415	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.6454	886	1415	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.3266	887	1415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:45,396] [INFO] DFAST Taxonomy check result was written to GCF_000615005.1_ASM61500v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:45,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:45,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:45,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference/checkm_data
[2024-01-24 12:40:45,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:45,443] [INFO] Task started: CheckM
[2024-01-24 12:40:45,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000615005.1_ASM61500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000615005.1_ASM61500v1_genomic.fna/checkm_input GCF_000615005.1_ASM61500v1_genomic.fna/checkm_result
[2024-01-24 12:41:19,091] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:19,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:19,111] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:19,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:19,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000615005.1_ASM61500v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:19,112] [INFO] Task started: Blastn
[2024-01-24 12:41:19,113] [INFO] Running command: blastn -query GCF_000615005.1_ASM61500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd97027f-c3a1-4474-a5a4-5b6058b625c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000615005.1_ASM61500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:20,173] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:20,176] [INFO] Selected 11 target genomes.
[2024-01-24 12:41:20,176] [INFO] Target genome list was writen to GCF_000615005.1_ASM61500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:20,185] [INFO] Task started: fastANI
[2024-01-24 12:41:20,185] [INFO] Running command: fastANI --query /var/lib/cwl/stgd81b26ac-89c2-4cdf-bdd7-0f7586937f89/GCF_000615005.1_ASM61500v1_genomic.fna.gz --refList GCF_000615005.1_ASM61500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000615005.1_ASM61500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:32,327] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:32,337] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:32,337] [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	99.941	1414	1415	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	86.3388	1107	1415	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	84.9609	1070	1415	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	84.7588	1079	1415	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	84.4204	1036	1415	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	84.3099	999	1415	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	83.9132	974	1415	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	82.1067	913	1415	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	81.9759	881	1415	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	81.9415	892	1415	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	81.6828	890	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:32,339] [INFO] GTDB search result was written to GCF_000615005.1_ASM61500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:32,339] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:32,344] [INFO] DFAST_QC result json was written to GCF_000615005.1_ASM61500v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:32,345] [INFO] DFAST_QC completed!
[2024-01-24 12:41:32,345] [INFO] Total running time: 0h1m12s