[2023-06-28 16:42:34,307] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:42:34,310] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:42:34,310] [INFO] DQC Reference Directory: /var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference
[2023-06-28 16:42:35,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:42:35,515] [INFO] Task started: Prodigal
[2023-06-28 16:42:35,516] [INFO] Running command: gunzip -c /var/lib/cwl/stg320b0fb4-5a14-4d69-af63-2da0bc8589be/GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:42:41,790] [INFO] Task succeeded: Prodigal
[2023-06-28 16:42:41,790] [INFO] Task started: HMMsearch
[2023-06-28 16:42:41,790] [INFO] Running command: hmmsearch --tblout GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference/reference_markers.hmm GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:42:42,047] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:42:42,049] [INFO] Found 6/6 markers.
[2023-06-28 16:42:42,084] [INFO] Query marker FASTA was written to GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 16:42:42,085] [INFO] Task started: Blastn
[2023-06-28 16:42:42,085] [INFO] Running command: blastn -query GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference/reference_markers.fasta -out GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:42:42,817] [INFO] Task succeeded: Blastn
[2023-06-28 16:42:42,822] [INFO] Selected 20 target genomes.
[2023-06-28 16:42:42,822] [INFO] Target genome list was writen to GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 16:42:42,828] [INFO] Task started: fastANI
[2023-06-28 16:42:42,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg320b0fb4-5a14-4d69-af63-2da0bc8589be/GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:42:52,728] [INFO] Task succeeded: fastANI
[2023-06-28 16:42:52,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:42:52,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:42:52,751] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:42:52,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:42:52,752] [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 baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	89.3735	648	826	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	84.521	646	826	95	below_threshold
Idiomarina fontislapidosi	strain=CECT 5859	GCA_003226255.1	263723	263723	type	True	84.3709	660	826	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	77.9208	109	826	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	77.911	112	826	95	below_threshold
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	77.9034	123	826	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	77.873	114	826	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	77.8207	145	826	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	77.6989	124	826	95	below_threshold
Pseudidiomarina atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	77.5031	66	826	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	77.4365	79	826	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	77.1827	59	826	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	77.1455	61	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:42:52,754] [INFO] DFAST Taxonomy check result was written to GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 16:42:52,755] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:42:52,755] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:42:52,756] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference/checkm_data
[2023-06-28 16:42:52,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:42:52,788] [INFO] Task started: CheckM
[2023-06-28 16:42:52,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 16:43:18,062] [INFO] Task succeeded: CheckM
[2023-06-28 16:43:18,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:43:18,085] [INFO] ===== Completeness check finished =====
[2023-06-28 16:43:18,085] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:43:18,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 16:43:18,086] [INFO] Task started: Blastn
[2023-06-28 16:43:18,086] [INFO] Running command: blastn -query GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgffe5841c-70cf-4c19-a5ad-1c35705857a5/dqc_reference/reference_markers_gtdb.fasta -out GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:19,221] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:19,225] [INFO] Selected 11 target genomes.
[2023-06-28 16:43:19,225] [INFO] Target genome list was writen to GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:43:19,268] [INFO] Task started: fastANI
[2023-06-28 16:43:19,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg320b0fb4-5a14-4d69-af63-2da0bc8589be/GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:43:24,851] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:24,865] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:43:24,865] [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
GCA_002685255.1	s__Idiomarina sp002685255	99.9652	808	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	conclusive
GCF_001870515.1	s__Idiomarina sp001870515	93.6152	777	826	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	89.3636	649	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	98.48	98.19	0.90	0.79	8	-
GCF_003226255.1	s__Idiomarina fontislapidosi	84.3709	660	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004362895.1	s__Idiomarina sp002729675	78.0508	135	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_900100855.1	s__Idiomarina zobellii	77.9617	112	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_002808045.1	s__Idiomarina sp002808045	77.7184	122	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_000008465.1	s__Idiomarina loihiensis	77.6989	124	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_000753735.1	s__Pseudidiomarina atlantica	77.5495	65	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	77.1313	58	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-28 16:43:24,867] [INFO] GTDB search result was written to GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 16:43:24,868] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:43:24,872] [INFO] DFAST_QC result json was written to GCA_913050225.1_ERR598965_bin.61_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 16:43:24,872] [INFO] DFAST_QC completed!
[2023-06-28 16:43:24,872] [INFO] Total running time: 0h0m51s