[2024-01-24 14:47:20,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:20,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:20,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference
[2024-01-24 14:47:21,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,201] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg722b17ae-01b7-4b17-9faa-d64760e748dd/GCF_003987185.1_ASM398718v1_genomic.fna.gz | prodigal -d GCF_003987185.1_ASM398718v1_genomic.fna/cds.fna -a GCF_003987185.1_ASM398718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:29,413] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:29,414] [INFO] Task started: HMMsearch
[2024-01-24 14:47:29,414] [INFO] Running command: hmmsearch --tblout GCF_003987185.1_ASM398718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference/reference_markers.hmm GCF_003987185.1_ASM398718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:29,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:29,673] [INFO] Found 6/6 markers.
[2024-01-24 14:47:29,701] [INFO] Query marker FASTA was written to GCF_003987185.1_ASM398718v1_genomic.fna/markers.fasta
[2024-01-24 14:47:29,702] [INFO] Task started: Blastn
[2024-01-24 14:47:29,702] [INFO] Running command: blastn -query GCF_003987185.1_ASM398718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference/reference_markers.fasta -out GCF_003987185.1_ASM398718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:30,509] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:30,512] [INFO] Selected 23 target genomes.
[2024-01-24 14:47:30,513] [INFO] Target genome list was writen to GCF_003987185.1_ASM398718v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:30,658] [INFO] Task started: fastANI
[2024-01-24 14:47:30,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg722b17ae-01b7-4b17-9faa-d64760e748dd/GCF_003987185.1_ASM398718v1_genomic.fna.gz --refList GCF_003987185.1_ASM398718v1_genomic.fna/target_genomes.txt --output GCF_003987185.1_ASM398718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:45,242] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:45,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:45,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:45,257] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:45,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:45,258] [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 aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	100.0	983	983	95	conclusive
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	80.1718	210	983	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	80.0428	317	983	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	79.9902	214	983	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	79.9786	98	983	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	79.6725	189	983	95	below_threshold
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	79.5001	169	983	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	79.4072	225	983	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	78.9311	95	983	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	78.232	101	983	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	77.632	94	983	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	77.463	92	983	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	77.1983	61	983	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:45,260] [INFO] DFAST Taxonomy check result was written to GCF_003987185.1_ASM398718v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:45,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:45,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:45,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference/checkm_data
[2024-01-24 14:47:45,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:45,298] [INFO] Task started: CheckM
[2024-01-24 14:47:45,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987185.1_ASM398718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987185.1_ASM398718v1_genomic.fna/checkm_input GCF_003987185.1_ASM398718v1_genomic.fna/checkm_result
[2024-01-24 14:48:17,633] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:17,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:17,657] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:17,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:17,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987185.1_ASM398718v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:17,659] [INFO] Task started: Blastn
[2024-01-24 14:48:17,659] [INFO] Running command: blastn -query GCF_003987185.1_ASM398718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc218bcf5-ead2-44cd-bf8c-7c69083134fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987185.1_ASM398718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:18,985] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:18,990] [INFO] Selected 21 target genomes.
[2024-01-24 14:48:18,990] [INFO] Target genome list was writen to GCF_003987185.1_ASM398718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:19,014] [INFO] Task started: fastANI
[2024-01-24 14:48:19,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg722b17ae-01b7-4b17-9faa-d64760e748dd/GCF_003987185.1_ASM398718v1_genomic.fna.gz --refList GCF_003987185.1_ASM398718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987185.1_ASM398718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:30,264] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:30,281] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:30,281] [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_003987185.1	s__Idiomarina aquatica	100.0	983	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	conclusive
GCF_004362895.1	s__Idiomarina sp002729675	80.6665	443	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_002808045.1	s__Idiomarina sp002808045	80.4568	198	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	80.0731	69	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987275.1	s__Idiomarina seosinensis	80.048	316	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100855.1	s__Idiomarina zobellii	80.0397	211	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	79.9467	99	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003987095.1	s__Idiomarina piscisalsi	79.6446	190	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152885.1	s__Idiomarina baltica	79.5001	169	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_000008465.1	s__Idiomarina loihiensis	79.4235	223	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_001870515.1	s__Idiomarina sp001870515	79.3264	171	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	79.2565	193	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003987215.1	s__Pseudidiomarina halophila	78.9445	96	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	78.6679	91	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	78.228	99	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	77.6243	53	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	77.2421	60	983	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:30,283] [INFO] GTDB search result was written to GCF_003987185.1_ASM398718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:30,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:30,288] [INFO] DFAST_QC result json was written to GCF_003987185.1_ASM398718v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:30,288] [INFO] DFAST_QC completed!
[2024-01-24 14:48:30,288] [INFO] Total running time: 0h1m10s