[2024-01-24 13:16:59,845] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:59,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:59,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference
[2024-01-24 13:17:01,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:01,172] [INFO] Task started: Prodigal
[2024-01-24 13:17:01,172] [INFO] Running command: gunzip -c /var/lib/cwl/stgbac07586-93c7-4be0-8df5-b128e9cd9af5/GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/cds.fna -a GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:08,927] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:08,928] [INFO] Task started: HMMsearch
[2024-01-24 13:17:08,928] [INFO] Running command: hmmsearch --tblout GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference/reference_markers.hmm GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:09,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:09,168] [INFO] Found 6/6 markers.
[2024-01-24 13:17:09,197] [INFO] Query marker FASTA was written to GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:17:09,197] [INFO] Task started: Blastn
[2024-01-24 13:17:09,197] [INFO] Running command: blastn -query GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference/reference_markers.fasta -out GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:10,689] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:10,692] [INFO] Selected 11 target genomes.
[2024-01-24 13:17:10,693] [INFO] Target genome list was writen to GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:17:10,696] [INFO] Task started: fastANI
[2024-01-24 13:17:10,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac07586-93c7-4be0-8df5-b128e9cd9af5/GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna.gz --refList GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:20,527] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:20,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:20,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:20,544] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:20,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:20,545] [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 carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	100.0	923	924	95	conclusive
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	86.9914	702	924	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	86.9713	704	924	95	below_threshold
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	86.7548	708	924	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	86.0563	696	924	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	85.5311	678	924	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0269	487	924	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.8928	457	924	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.8807	457	924	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.4144	393	924	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	78.3146	358	924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:20,547] [INFO] DFAST Taxonomy check result was written to GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:17:20,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:20,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:20,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference/checkm_data
[2024-01-24 13:17:20,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:20,576] [INFO] Task started: CheckM
[2024-01-24 13:17:20,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/checkm_input GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:18:02,431] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:02,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,454] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:02,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:02,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:18:02,455] [INFO] Task started: Blastn
[2024-01-24 13:18:02,455] [INFO] Running command: blastn -query GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb36db9b0-0b79-483b-91d8-83b1e2818b5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:04,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:04,972] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:04,973] [INFO] Target genome list was writen to GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:04,986] [INFO] Task started: fastANI
[2024-01-24 13:18:04,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgbac07586-93c7-4be0-8df5-b128e9cd9af5/GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna.gz --refList GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:13,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:13,787] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:13,787] [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_900104705.1	s__Agrococcus carbonis	100.0	923	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007988785.1	s__Agrococcus baldri_A	87.2037	723	924	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	86.9643	703	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.37	97.37	0.91	0.91	2	-
GCF_000425105.1	s__Agrococcus lahaulensis	86.9462	706	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018308945.1	s__Agrococcus sp018308945	86.8228	692	924	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	86.795	705	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	-
GCA_900114805.1	s__Agrococcus baldri	86.3297	717	924	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	86.2423	718	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752465.1	s__Agrococcus jenensis	86.0275	698	924	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117395.1	s__Agrococcus sp900117395	85.8445	700	924	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 13:18:13,789] [INFO] GTDB search result was written to GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:13,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:13,792] [INFO] DFAST_QC result json was written to GCF_900104705.1_IMG-taxon_2634166154_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:18:13,793] [INFO] DFAST_QC completed!
[2024-01-24 13:18:13,793] [INFO] Total running time: 0h1m14s