[2024-01-24 13:49:00,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:00,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:00,423] [INFO] DQC Reference Directory: /var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference
[2024-01-24 13:49:01,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,722] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bf83fe9-5fa1-4d2e-aba0-7021d28f93b5/GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/cds.fna -a GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:11,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:11,836] [INFO] Task started: HMMsearch
[2024-01-24 13:49:11,837] [INFO] Running command: hmmsearch --tblout GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference/reference_markers.hmm GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:12,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:12,080] [INFO] Found 6/6 markers.
[2024-01-24 13:49:12,111] [INFO] Query marker FASTA was written to GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:12,112] [INFO] Task started: Blastn
[2024-01-24 13:49:12,112] [INFO] Running command: blastn -query GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference/reference_markers.fasta -out GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:13,340] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:13,343] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:13,343] [INFO] Target genome list was writen to GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:13,377] [INFO] Task started: fastANI
[2024-01-24 13:49:13,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf83fe9-5fa1-4d2e-aba0-7021d28f93b5/GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna.gz --refList GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:24,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:24,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:24,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:24,400] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:24,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:24,400] [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
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	100.0	1132	1133	95	conclusive
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	82.2717	648	1133	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	81.7411	593	1133	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	81.7381	601	1133	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	81.6511	609	1133	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	81.6085	603	1133	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	81.5604	633	1133	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.4954	517	1133	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.3686	425	1133	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	78.3619	487	1133	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	78.2412	457	1133	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.5918	445	1133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:24,403] [INFO] DFAST Taxonomy check result was written to GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:24,404] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:24,404] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:24,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference/checkm_data
[2024-01-24 13:49:24,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:24,444] [INFO] Task started: CheckM
[2024-01-24 13:49:24,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/checkm_input GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:26,913] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:26,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,942] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:26,943] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:26,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:26,944] [INFO] Task started: Blastn
[2024-01-24 13:50:26,944] [INFO] Running command: blastn -query GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf480d8da-1d1e-4124-9cbd-ededc1818592/dqc_reference/reference_markers_gtdb.fasta -out GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:28,966] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:28,970] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:28,970] [INFO] Target genome list was writen to GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:28,977] [INFO] Task started: fastANI
[2024-01-24 13:50:28,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bf83fe9-5fa1-4d2e-aba0-7021d28f93b5/GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna.gz --refList GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:38,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:38,940] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:38,940] [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_900099705.1	s__Agrococcus jejuensis	100.0	1131	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007679035.1	s__Agrococcus jejuensis_A	92.2973	984	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484985.1	s__Agrococcus sp005484985	88.575	885	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645235.1	s__Agrococcus terreus	82.2309	651	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923295.1	s__Agrococcus sediminis	81.8079	588	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	-
GCF_900104705.1	s__Agrococcus carbonis	81.6971	604	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400485.1	s__Agrococcus pavilionensis	81.6882	606	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.37	97.37	0.91	0.91	2	-
GCF_003752465.1	s__Agrococcus jenensis	81.4971	642	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168255.1	s__Agrococcus sp017168255	80.3847	555	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,942] [INFO] GTDB search result was written to GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:38,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:38,946] [INFO] DFAST_QC result json was written to GCF_900099705.1_IMG-taxon_2634166279_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:38,946] [INFO] DFAST_QC completed!
[2024-01-24 13:50:38,946] [INFO] Total running time: 0h1m39s