[2024-01-25 18:09:20,352] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:20,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:20,353] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference
[2024-01-25 18:09:21,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:21,481] [INFO] Task started: Prodigal
[2024-01-25 18:09:21,481] [INFO] Running command: gunzip -c /var/lib/cwl/stga5a661ee-0ffc-4a9a-b6c6-0534290f3f89/GCF_003752465.1_ASM375246v1_genomic.fna.gz | prodigal -d GCF_003752465.1_ASM375246v1_genomic.fna/cds.fna -a GCF_003752465.1_ASM375246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:28,691] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:28,691] [INFO] Task started: HMMsearch
[2024-01-25 18:09:28,691] [INFO] Running command: hmmsearch --tblout GCF_003752465.1_ASM375246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference/reference_markers.hmm GCF_003752465.1_ASM375246v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:28,898] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:28,899] [INFO] Found 6/6 markers.
[2024-01-25 18:09:28,923] [INFO] Query marker FASTA was written to GCF_003752465.1_ASM375246v1_genomic.fna/markers.fasta
[2024-01-25 18:09:28,923] [INFO] Task started: Blastn
[2024-01-25 18:09:28,923] [INFO] Running command: blastn -query GCF_003752465.1_ASM375246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference/reference_markers.fasta -out GCF_003752465.1_ASM375246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:30,064] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:30,066] [INFO] Selected 11 target genomes.
[2024-01-25 18:09:30,066] [INFO] Target genome list was writen to GCF_003752465.1_ASM375246v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:30,072] [INFO] Task started: fastANI
[2024-01-25 18:09:30,072] [INFO] Running command: fastANI --query /var/lib/cwl/stga5a661ee-0ffc-4a9a-b6c6-0534290f3f89/GCF_003752465.1_ASM375246v1_genomic.fna.gz --refList GCF_003752465.1_ASM375246v1_genomic.fna/target_genomes.txt --output GCF_003752465.1_ASM375246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:38,812] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:38,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:38,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:38,820] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:38,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:38,821] [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 jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	100.0	987	987	95	conclusive
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	87.0607	721	987	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	86.3883	700	987	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	86.228	705	987	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	86.0964	700	987	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	85.6426	750	987	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.8674	494	987	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.743	403	987	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.6837	467	987	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	78.6356	414	987	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.4524	365	987	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:38,822] [INFO] DFAST Taxonomy check result was written to GCF_003752465.1_ASM375246v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:38,822] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:38,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:38,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference/checkm_data
[2024-01-25 18:09:38,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:38,854] [INFO] Task started: CheckM
[2024-01-25 18:09:38,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003752465.1_ASM375246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003752465.1_ASM375246v1_genomic.fna/checkm_input GCF_003752465.1_ASM375246v1_genomic.fna/checkm_result
[2024-01-25 18:10:21,146] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:21,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:21,171] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:21,172] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:21,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003752465.1_ASM375246v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:21,173] [INFO] Task started: Blastn
[2024-01-25 18:10:21,173] [INFO] Running command: blastn -query GCF_003752465.1_ASM375246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c859c0e-f8c8-4483-b11c-cc060859d8f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003752465.1_ASM375246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:23,179] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:23,183] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:23,183] [INFO] Target genome list was writen to GCF_003752465.1_ASM375246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:23,190] [INFO] Task started: fastANI
[2024-01-25 18:10:23,190] [INFO] Running command: fastANI --query /var/lib/cwl/stga5a661ee-0ffc-4a9a-b6c6-0534290f3f89/GCF_003752465.1_ASM375246v1_genomic.fna.gz --refList GCF_003752465.1_ASM375246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003752465.1_ASM375246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:32,014] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:32,021] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:32,021] [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_003752465.1	s__Agrococcus jenensis	100.0	987	987	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	87.1127	718	987	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	86.3553	702	987	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	86.2835	701	987	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	86.0469	703	987	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	85.9725	705	987	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	85.6619	749	987	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	85.5768	702	987	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	85.2326	732	987	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	84.6903	688	987	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 18:10:32,023] [INFO] GTDB search result was written to GCF_003752465.1_ASM375246v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:32,023] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:32,026] [INFO] DFAST_QC result json was written to GCF_003752465.1_ASM375246v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:32,026] [INFO] DFAST_QC completed!
[2024-01-25 18:10:32,026] [INFO] Total running time: 0h1m12s