[2024-01-24 12:31:32,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:32,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:32,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference
[2024-01-24 12:31:33,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:33,864] [INFO] Task started: Prodigal
[2024-01-24 12:31:33,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg28ddd7e4-6bb2-4d70-bab5-3719907f93f9/GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/cds.fna -a GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:50,382] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:50,382] [INFO] Task started: HMMsearch
[2024-01-24 12:31:50,383] [INFO] Running command: hmmsearch --tblout GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference/reference_markers.hmm GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:50,645] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:50,646] [INFO] Found 6/6 markers.
[2024-01-24 12:31:50,691] [INFO] Query marker FASTA was written to GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:50,691] [INFO] Task started: Blastn
[2024-01-24 12:31:50,691] [INFO] Running command: blastn -query GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference/reference_markers.fasta -out GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:51,236] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:51,238] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:51,239] [INFO] Target genome list was writen to GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:51,244] [INFO] Task started: fastANI
[2024-01-24 12:31:51,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ddd7e4-6bb2-4d70-bab5-3719907f93f9/GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna.gz --refList GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:13,681] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:13,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:13,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:13,690] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:13,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:13,690] [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
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	100.0	2081	2084	95	conclusive
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.165	211	2084	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	76.151	183	2084	95	below_threshold
Thalassoglobus neptunius	strain=KOR42	GCA_007859735.1	1938619	1938619	type	True	76.0669	68	2084	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.7484	62	2084	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.6946	53	2084	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	75.6463	87	2084	95	below_threshold
Calycomorphotria hydatis	strain=V22	GCA_007745435.1	2528027	2528027	type	True	75.3693	72	2084	95	below_threshold
Schlesneria paludicola	strain=DSM 18645	GCA_000255655.1	360056	360056	type	True	75.3065	66	2084	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.1036	54	2084	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9021	73	2084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:13,691] [INFO] DFAST Taxonomy check result was written to GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:13,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:13,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:13,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference/checkm_data
[2024-01-24 12:32:13,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:13,752] [INFO] Task started: CheckM
[2024-01-24 12:32:13,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/checkm_input GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:33:04,125] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:04,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:04,144] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:04,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:04,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:33:04,145] [INFO] Task started: Blastn
[2024-01-24 12:33:04,145] [INFO] Running command: blastn -query GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcb010d6-456d-4c3d-ad32-77753f1f7640/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:04,950] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:04,952] [INFO] Selected 26 target genomes.
[2024-01-24 12:33:04,953] [INFO] Target genome list was writen to GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:05,010] [INFO] Task started: fastANI
[2024-01-24 12:33:05,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg28ddd7e4-6bb2-4d70-bab5-3719907f93f9/GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna.gz --refList GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:28,158] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:28,166] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:28,167] [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_900113665.1	s__Planctomicrobium piriforme	100.0	2081	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003388505.1	s__MB-PLM-1 sp003388505	76.2599	146	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCF_001610835.1	s__Planctomyces_A sp001610835	76.2225	186	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	76.2189	203	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	76.1332	185	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859735.1	s__Thalassoglobus neptunius	76.0669	68	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Thalassoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.8877	107	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.8444	75	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.668	124	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165715.2	s__Rubinisphaera brasiliensis	75.6589	86	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.6042	92	2084	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464385.1	s__Ga0077550 sp001464385	74.6842	55	2084	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:28,168] [INFO] GTDB search result was written to GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:28,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:28,171] [INFO] DFAST_QC result json was written to GCF_900113665.1_IMG-taxon_2675903691_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:33:28,171] [INFO] DFAST_QC completed!
[2024-01-24 12:33:28,171] [INFO] Total running time: 0h1m55s