[2024-01-24 11:05:25,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,254] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,254] [INFO] DQC Reference Directory: /var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference
[2024-01-24 11:05:26,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,792] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,793] [INFO] Running command: gunzip -c /var/lib/cwl/stge44eff63-a074-4887-a2f8-f29e574cb939/GCF_003987025.1_ASM398702v1_genomic.fna.gz | prodigal -d GCF_003987025.1_ASM398702v1_genomic.fna/cds.fna -a GCF_003987025.1_ASM398702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:34,060] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:34,060] [INFO] Task started: HMMsearch
[2024-01-24 11:05:34,060] [INFO] Running command: hmmsearch --tblout GCF_003987025.1_ASM398702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference/reference_markers.hmm GCF_003987025.1_ASM398702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:34,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:34,338] [INFO] Found 6/6 markers.
[2024-01-24 11:05:34,366] [INFO] Query marker FASTA was written to GCF_003987025.1_ASM398702v1_genomic.fna/markers.fasta
[2024-01-24 11:05:34,367] [INFO] Task started: Blastn
[2024-01-24 11:05:34,367] [INFO] Running command: blastn -query GCF_003987025.1_ASM398702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference/reference_markers.fasta -out GCF_003987025.1_ASM398702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:35,123] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:35,128] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:35,128] [INFO] Target genome list was writen to GCF_003987025.1_ASM398702v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:35,138] [INFO] Task started: fastANI
[2024-01-24 11:05:35,138] [INFO] Running command: fastANI --query /var/lib/cwl/stge44eff63-a074-4887-a2f8-f29e574cb939/GCF_003987025.1_ASM398702v1_genomic.fna.gz --refList GCF_003987025.1_ASM398702v1_genomic.fna/target_genomes.txt --output GCF_003987025.1_ASM398702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:45,094] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:45,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:45,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:45,106] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:45,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:45,107] [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
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	100.0	936	937	95	conclusive
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	99.9955	918	937	95	conclusive
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	83.552	629	937	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	78.8018	125	937	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	78.4976	152	937	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	78.4852	111	937	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	78.3355	131	937	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	78.3162	133	937	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	78.0167	89	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:45,108] [INFO] DFAST Taxonomy check result was written to GCF_003987025.1_ASM398702v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:45,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:45,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:45,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference/checkm_data
[2024-01-24 11:05:45,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:45,141] [INFO] Task started: CheckM
[2024-01-24 11:05:45,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987025.1_ASM398702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987025.1_ASM398702v1_genomic.fna/checkm_input GCF_003987025.1_ASM398702v1_genomic.fna/checkm_result
[2024-01-24 11:06:12,606] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:12,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:12,628] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:12,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:12,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987025.1_ASM398702v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:12,629] [INFO] Task started: Blastn
[2024-01-24 11:06:12,629] [INFO] Running command: blastn -query GCF_003987025.1_ASM398702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01921307-3a43-4940-82d4-2dec6f04f23d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987025.1_ASM398702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:13,754] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:13,757] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:13,757] [INFO] Target genome list was writen to GCF_003987025.1_ASM398702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:13,764] [INFO] Task started: fastANI
[2024-01-24 11:06:13,765] [INFO] Running command: fastANI --query /var/lib/cwl/stge44eff63-a074-4887-a2f8-f29e574cb939/GCF_003987025.1_ASM398702v1_genomic.fna.gz --refList GCF_003987025.1_ASM398702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987025.1_ASM398702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:19,702] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:19,714] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:19,714] [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_003226255.1	s__Idiomarina fontislapidosi	99.9955	918	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001870515.1	s__Idiomarina sp001870515	84.5092	682	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685255.1	s__Idiomarina sp002685255	84.41	679	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
GCF_000152885.1	s__Idiomarina baltica	83.5374	629	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_004362895.1	s__Idiomarina sp002729675	79.5659	166	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003987095.1	s__Idiomarina piscisalsi	78.8018	125	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987275.1	s__Idiomarina seosinensis	78.5224	151	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	78.3355	131	937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:19,716] [INFO] GTDB search result was written to GCF_003987025.1_ASM398702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:19,716] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:19,721] [INFO] DFAST_QC result json was written to GCF_003987025.1_ASM398702v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:19,721] [INFO] DFAST_QC completed!
[2024-01-24 11:06:19,721] [INFO] Total running time: 0h0m54s