[2024-01-24 13:40:35,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference
[2024-01-24 13:40:36,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,657] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgee8ffaf0-763e-4441-aebe-2e26211e849c/GCF_007748035.1_ASM774803v1_genomic.fna.gz | prodigal -d GCF_007748035.1_ASM774803v1_genomic.fna/cds.fna -a GCF_007748035.1_ASM774803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:00,174] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:00,174] [INFO] Task started: HMMsearch
[2024-01-24 13:41:00,174] [INFO] Running command: hmmsearch --tblout GCF_007748035.1_ASM774803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference/reference_markers.hmm GCF_007748035.1_ASM774803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:00,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:00,587] [INFO] Found 6/6 markers.
[2024-01-24 13:41:00,640] [INFO] Query marker FASTA was written to GCF_007748035.1_ASM774803v1_genomic.fna/markers.fasta
[2024-01-24 13:41:00,640] [INFO] Task started: Blastn
[2024-01-24 13:41:00,640] [INFO] Running command: blastn -query GCF_007748035.1_ASM774803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference/reference_markers.fasta -out GCF_007748035.1_ASM774803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:01,269] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:01,272] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:01,273] [INFO] Target genome list was writen to GCF_007748035.1_ASM774803v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:01,287] [INFO] Task started: fastANI
[2024-01-24 13:41:01,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8ffaf0-763e-4441-aebe-2e26211e849c/GCF_007748035.1_ASM774803v1_genomic.fna.gz --refList GCF_007748035.1_ASM774803v1_genomic.fna/target_genomes.txt --output GCF_007748035.1_ASM774803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:20,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:20,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:20,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:20,313] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:20,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:20,314] [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
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	100.0	2202	2202	95	conclusive
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.6205	194	2202	95	below_threshold
Adhaeretor mobilis	strain=HG15A2	GCA_007741515.1	1930276	1930276	type	True	76.5873	86	2202	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.5826	251	2202	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.5816	245	2202	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.5172	113	2202	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.2937	196	2202	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.2838	164	2202	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	76.144	131	2202	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.953	88	2202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:20,316] [INFO] DFAST Taxonomy check result was written to GCF_007748035.1_ASM774803v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:20,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:20,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:20,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference/checkm_data
[2024-01-24 13:41:20,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:20,381] [INFO] Task started: CheckM
[2024-01-24 13:41:20,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007748035.1_ASM774803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007748035.1_ASM774803v1_genomic.fna/checkm_input GCF_007748035.1_ASM774803v1_genomic.fna/checkm_result
[2024-01-24 13:42:24,195] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:24,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,220] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:24,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:24,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007748035.1_ASM774803v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:24,221] [INFO] Task started: Blastn
[2024-01-24 13:42:24,221] [INFO] Running command: blastn -query GCF_007748035.1_ASM774803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg326fe614-31c2-42c8-a953-d6a6c6eef339/dqc_reference/reference_markers_gtdb.fasta -out GCF_007748035.1_ASM774803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:25,048] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:25,053] [INFO] Selected 22 target genomes.
[2024-01-24 13:42:25,054] [INFO] Target genome list was writen to GCF_007748035.1_ASM774803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:25,129] [INFO] Task started: fastANI
[2024-01-24 13:42:25,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8ffaf0-763e-4441-aebe-2e26211e849c/GCF_007748035.1_ASM774803v1_genomic.fna.gz --refList GCF_007748035.1_ASM774803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007748035.1_ASM774803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:46,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:46,795] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:46,795] [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_007748035.1	s__Aeoliella mucimassa	100.0	2202	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Aeoliella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859945.1	s__Pseudobythopirellula maris	76.6211	194	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	76.5996	243	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	76.5914	250	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741515.1	s__HG15A2 sp007741515	76.5873	86	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__HG15A2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003233055.1	s__Aeoliella sp003233055	76.3978	119	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Aeoliella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	76.3188	205	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	76.3124	159	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	76.2936	196	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	76.2837	164	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	76.1259	109	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931995.1	s__JAFGDS01 sp016931995	75.445	65	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464525.1	s__Ga0077529 sp001464525	75.4187	88	2202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Ga0077529	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:46,796] [INFO] GTDB search result was written to GCF_007748035.1_ASM774803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:46,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:46,801] [INFO] DFAST_QC result json was written to GCF_007748035.1_ASM774803v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:46,801] [INFO] DFAST_QC completed!
[2024-01-24 13:42:46,801] [INFO] Total running time: 0h2m12s