[2024-01-25 18:53:05,774] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:05,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:05,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference
[2024-01-25 18:53:06,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:06,907] [INFO] Task started: Prodigal
[2024-01-25 18:53:06,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc7e5b27-893a-4923-aaf1-0b8f03b84a1f/GCF_014645235.1_ASM1464523v1_genomic.fna.gz | prodigal -d GCF_014645235.1_ASM1464523v1_genomic.fna/cds.fna -a GCF_014645235.1_ASM1464523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:13,631] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:13,631] [INFO] Task started: HMMsearch
[2024-01-25 18:53:13,631] [INFO] Running command: hmmsearch --tblout GCF_014645235.1_ASM1464523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference/reference_markers.hmm GCF_014645235.1_ASM1464523v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:13,841] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:13,842] [INFO] Found 6/6 markers.
[2024-01-25 18:53:13,867] [INFO] Query marker FASTA was written to GCF_014645235.1_ASM1464523v1_genomic.fna/markers.fasta
[2024-01-25 18:53:13,867] [INFO] Task started: Blastn
[2024-01-25 18:53:13,867] [INFO] Running command: blastn -query GCF_014645235.1_ASM1464523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference/reference_markers.fasta -out GCF_014645235.1_ASM1464523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:15,052] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:15,056] [INFO] Selected 11 target genomes.
[2024-01-25 18:53:15,056] [INFO] Target genome list was writen to GCF_014645235.1_ASM1464523v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:15,063] [INFO] Task started: fastANI
[2024-01-25 18:53:15,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7e5b27-893a-4923-aaf1-0b8f03b84a1f/GCF_014645235.1_ASM1464523v1_genomic.fna.gz --refList GCF_014645235.1_ASM1464523v1_genomic.fna/target_genomes.txt --output GCF_014645235.1_ASM1464523v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:24,757] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:24,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:24,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:24,766] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:24,766] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:24,766] [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 terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	100.0	939	940	95	conclusive
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	86.2084	703	940	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	85.7497	668	940	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	85.719	744	940	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	85.5999	671	940	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	85.377	692	940	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.6676	487	940	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	78.0672	387	940	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.0069	451	940	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.6375	388	940	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.6043	412	940	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:24,772] [INFO] DFAST Taxonomy check result was written to GCF_014645235.1_ASM1464523v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:24,772] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:24,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:24,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference/checkm_data
[2024-01-25 18:53:24,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:24,803] [INFO] Task started: CheckM
[2024-01-25 18:53:24,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645235.1_ASM1464523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645235.1_ASM1464523v1_genomic.fna/checkm_input GCF_014645235.1_ASM1464523v1_genomic.fna/checkm_result
[2024-01-25 18:54:02,652] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:02,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:02,706] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:02,706] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:02,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645235.1_ASM1464523v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:02,708] [INFO] Task started: Blastn
[2024-01-25 18:54:02,708] [INFO] Running command: blastn -query GCF_014645235.1_ASM1464523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee146131-5c28-48a9-a7f1-dfc8423a045b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645235.1_ASM1464523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:04,673] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:04,675] [INFO] Selected 10 target genomes.
[2024-01-25 18:54:04,675] [INFO] Target genome list was writen to GCF_014645235.1_ASM1464523v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:04,707] [INFO] Task started: fastANI
[2024-01-25 18:54:04,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7e5b27-893a-4923-aaf1-0b8f03b84a1f/GCF_014645235.1_ASM1464523v1_genomic.fna.gz --refList GCF_014645235.1_ASM1464523v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645235.1_ASM1464523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:13,591] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:13,598] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:13,598] [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_014645235.1	s__Agrococcus terreus	100.0	939	940	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_007923295.1	s__Agrococcus sediminis	86.1794	705	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	-
GCF_000400485.1	s__Agrococcus pavilionensis	85.7528	667	940	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	85.7491	742	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425105.1	s__Agrococcus lahaulensis	85.615	670	940	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	85.4114	667	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104705.1	s__Agrococcus carbonis	85.3726	692	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007988785.1	s__Agrococcus baldri_A	84.8568	697	940	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	83.9443	653	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900114805.1	s__Agrococcus baldri	83.9203	673	940	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:13,600] [INFO] GTDB search result was written to GCF_014645235.1_ASM1464523v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:13,600] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:13,603] [INFO] DFAST_QC result json was written to GCF_014645235.1_ASM1464523v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:13,603] [INFO] DFAST_QC completed!
[2024-01-25 18:54:13,603] [INFO] Total running time: 0h1m8s