[2024-01-24 15:18:27,321] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,323] [INFO] DQC Reference Directory: /var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference
[2024-01-24 15:18:28,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,664] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,664] [INFO] Running command: gunzip -c /var/lib/cwl/stgc56f6439-1752-4686-a67e-49cdb23970b7/GCF_007746075.1_ASM774607v1_genomic.fna.gz | prodigal -d GCF_007746075.1_ASM774607v1_genomic.fna/cds.fna -a GCF_007746075.1_ASM774607v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:48,705] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:48,705] [INFO] Task started: HMMsearch
[2024-01-24 15:18:48,705] [INFO] Running command: hmmsearch --tblout GCF_007746075.1_ASM774607v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference/reference_markers.hmm GCF_007746075.1_ASM774607v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:49,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:49,024] [INFO] Found 6/6 markers.
[2024-01-24 15:18:49,082] [INFO] Query marker FASTA was written to GCF_007746075.1_ASM774607v1_genomic.fna/markers.fasta
[2024-01-24 15:18:49,083] [INFO] Task started: Blastn
[2024-01-24 15:18:49,083] [INFO] Running command: blastn -query GCF_007746075.1_ASM774607v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference/reference_markers.fasta -out GCF_007746075.1_ASM774607v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,703] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,707] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:49,707] [INFO] Target genome list was writen to GCF_007746075.1_ASM774607v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:49,713] [INFO] Task started: fastANI
[2024-01-24 15:18:49,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgc56f6439-1752-4686-a67e-49cdb23970b7/GCF_007746075.1_ASM774607v1_genomic.fna.gz --refList GCF_007746075.1_ASM774607v1_genomic.fna/target_genomes.txt --output GCF_007746075.1_ASM774607v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:07,619] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:07,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:07,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:07,636] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:07,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:07,637] [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
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	100.0	2276	2276	95	conclusive
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	81.043	1108	2276	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.8046	253	2276	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.7693	260	2276	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.7656	230	2276	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	76.7503	250	2276	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.6991	246	2276	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.612	266	2276	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	76.2008	130	2276	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	74.7027	60	2276	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	74.7025	72	2276	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	74.5653	85	2276	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	74.5645	84	2276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:07,638] [INFO] DFAST Taxonomy check result was written to GCF_007746075.1_ASM774607v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:07,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:07,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:07,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference/checkm_data
[2024-01-24 15:19:07,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:07,704] [INFO] Task started: CheckM
[2024-01-24 15:19:07,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007746075.1_ASM774607v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007746075.1_ASM774607v1_genomic.fna/checkm_input GCF_007746075.1_ASM774607v1_genomic.fna/checkm_result
[2024-01-24 15:20:02,777] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:02,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:02,801] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:02,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:02,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007746075.1_ASM774607v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:02,802] [INFO] Task started: Blastn
[2024-01-24 15:20:02,802] [INFO] Running command: blastn -query GCF_007746075.1_ASM774607v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb00d1742-09d6-4514-87c2-3b572b3bf395/dqc_reference/reference_markers_gtdb.fasta -out GCF_007746075.1_ASM774607v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:03,639] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:03,642] [INFO] Selected 14 target genomes.
[2024-01-24 15:20:03,642] [INFO] Target genome list was writen to GCF_007746075.1_ASM774607v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:03,652] [INFO] Task started: fastANI
[2024-01-24 15:20:03,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgc56f6439-1752-4686-a67e-49cdb23970b7/GCF_007746075.1_ASM774607v1_genomic.fna.gz --refList GCF_007746075.1_ASM774607v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007746075.1_ASM774607v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:21,203] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:21,218] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:21,218] [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_007746075.1	s__Lacipirellula limnantheis	100.0	2276	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	97.19	97.19	0.90	0.90	2	conclusive
GCA_013822725.1	s__Lacipirellula sp013822725	83.6858	1117	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	81.0235	1112	2276	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	77.3118	431	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	76.7962	255	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	76.7568	231	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	76.6973	246	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	76.6757	351	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	76.588	269	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152515.1	s__Bythopirellula sp013152515	76.1509	91	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576845.1	s__PLA5 sp003576845	75.8679	180	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PLA5;g__PLA5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	75.6241	128	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200205.1	s__PALSA-1355 sp016200205	75.5341	75	2276	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__PALSA-1355	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:21,220] [INFO] GTDB search result was written to GCF_007746075.1_ASM774607v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:21,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:21,224] [INFO] DFAST_QC result json was written to GCF_007746075.1_ASM774607v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:21,224] [INFO] DFAST_QC completed!
[2024-01-24 15:20:21,224] [INFO] Total running time: 0h1m54s