[2024-01-24 11:21:07,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference
[2024-01-24 11:21:11,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,974] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg78036bff-2a07-4680-affd-9be1303fcdb2/GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/cds.fna -a GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:24,887] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:24,888] [INFO] Task started: HMMsearch
[2024-01-24 11:21:24,888] [INFO] Running command: hmmsearch --tblout GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference/reference_markers.hmm GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:25,164] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:25,166] [INFO] Found 6/6 markers.
[2024-01-24 11:21:25,214] [INFO] Query marker FASTA was written to GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:21:25,215] [INFO] Task started: Blastn
[2024-01-24 11:21:25,215] [INFO] Running command: blastn -query GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference/reference_markers.fasta -out GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:26,416] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:26,420] [INFO] Selected 16 target genomes.
[2024-01-24 11:21:26,420] [INFO] Target genome list was writen to GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:21:26,427] [INFO] Task started: fastANI
[2024-01-24 11:21:26,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg78036bff-2a07-4680-affd-9be1303fcdb2/GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna.gz --refList GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:41,826] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:41,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:41,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:41,841] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:21:41,841] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:21:41,841] [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
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	80.1253	794	1572	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	80.0486	720	1572	95	below_threshold
Microlunatus flavus	strain=CGMCC 4.6856	GCA_900110855.1	1036181	1036181	type	True	79.9255	809	1572	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	79.7675	668	1572	95	below_threshold
Microlunatus panaciterrae	strain=DSM 18662	GCA_016907535.1	400768	400768	type	True	79.1336	538	1572	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	79.039	532	1572	95	below_threshold
Microlunatus phosphovorus	strain=NM-1	GCA_000270245.1	29405	29405	type	True	78.8245	502	1572	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.803	631	1572	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	78.7108	615	1572	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.7048	647	1572	95	below_threshold
Microlunatus parietis	strain=DSM 22083	GCA_013407955.1	682979	682979	type	True	78.325	627	1572	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	78.2456	607	1572	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.5279	501	1572	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.2883	410	1572	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	77.1131	426	1572	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	77.0798	455	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:41,843] [INFO] DFAST Taxonomy check result was written to GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:21:41,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:41,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:41,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference/checkm_data
[2024-01-24 11:21:41,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:41,888] [INFO] Task started: CheckM
[2024-01-24 11:21:41,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/checkm_input GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:22:54,619] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:54,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:54,640] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:54,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:54,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:22:54,641] [INFO] Task started: Blastn
[2024-01-24 11:22:54,641] [INFO] Running command: blastn -query GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6fd19d4-b6e4-4f0f-a25e-2fc2715e37e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:56,529] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:56,533] [INFO] Selected 10 target genomes.
[2024-01-24 11:22:56,533] [INFO] Target genome list was writen to GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:56,541] [INFO] Task started: fastANI
[2024-01-24 11:22:56,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg78036bff-2a07-4680-affd-9be1303fcdb2/GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna.gz --refList GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:23:07,643] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:07,655] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:23:07,655] [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_900105065.1	s__Friedmanniella luteola	100.0	1570	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017876495.1	s__Friedmanniella capsulata	87.6723	1177	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105785.1	s__Friedmanniella sagamiharensis	80.139	792	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907175.1	s__Friedmanniella spumicola	80.1196	795	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193425.1	s__Friedmanniella antarctica	80.0901	719	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110855.1	s__Friedmanniella flava	79.8647	818	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137855.1	s__Friedmanniella_A endophytica	79.7341	673	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907535.1	s__Microlunatus_C panaciterrae	79.115	540	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805915.1	s__CADCUO01 sp902805915	78.7887	415	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__CADCUO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299835.1	s__Microlunatus_B speluncae	78.2449	607	1572	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:23:07,656] [INFO] GTDB search result was written to GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:23:07,657] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:23:07,665] [INFO] DFAST_QC result json was written to GCF_900105065.1_IMG-taxon_2630969010_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:23:07,666] [INFO] DFAST_QC completed!
[2024-01-24 11:23:07,666] [INFO] Total running time: 0h2m0s