[2024-01-24 13:40:55,536] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference
[2024-01-24 13:40:56,776] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,777] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,777] [INFO] Running command: gunzip -c /var/lib/cwl/stg2811b96a-359d-455a-b420-52e3a3fdaec3/GCF_900292075.1_PRJEB24954_genomic.fna.gz | prodigal -d GCF_900292075.1_PRJEB24954_genomic.fna/cds.fna -a GCF_900292075.1_PRJEB24954_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:07,334] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:07,334] [INFO] Task started: HMMsearch
[2024-01-24 13:41:07,334] [INFO] Running command: hmmsearch --tblout GCF_900292075.1_PRJEB24954_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference/reference_markers.hmm GCF_900292075.1_PRJEB24954_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:07,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:07,625] [INFO] Found 6/6 markers.
[2024-01-24 13:41:07,671] [INFO] Query marker FASTA was written to GCF_900292075.1_PRJEB24954_genomic.fna/markers.fasta
[2024-01-24 13:41:07,671] [INFO] Task started: Blastn
[2024-01-24 13:41:07,671] [INFO] Running command: blastn -query GCF_900292075.1_PRJEB24954_genomic.fna/markers.fasta -db /var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference/reference_markers.fasta -out GCF_900292075.1_PRJEB24954_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:08,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:08,766] [INFO] Selected 11 target genomes.
[2024-01-24 13:41:08,766] [INFO] Target genome list was writen to GCF_900292075.1_PRJEB24954_genomic.fna/target_genomes.txt
[2024-01-24 13:41:08,769] [INFO] Task started: fastANI
[2024-01-24 13:41:08,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg2811b96a-359d-455a-b420-52e3a3fdaec3/GCF_900292075.1_PRJEB24954_genomic.fna.gz --refList GCF_900292075.1_PRJEB24954_genomic.fna/target_genomes.txt --output GCF_900292075.1_PRJEB24954_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:19,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:19,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:19,801] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:19,802] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:19,802] [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
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	100.0	1315	1315	95	conclusive
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	83.8647	812	1315	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	83.8259	895	1315	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	83.664	904	1315	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	83.4995	808	1315	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	83.3354	899	1315	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	83.268	852	1315	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	83.1283	857	1315	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	83.1172	842	1315	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.132	707	1315	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	81.94	721	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,804] [INFO] DFAST Taxonomy check result was written to GCF_900292075.1_PRJEB24954_genomic.fna/tc_result.tsv
[2024-01-24 13:41:19,805] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:19,805] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:19,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference/checkm_data
[2024-01-24 13:41:19,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:19,849] [INFO] Task started: CheckM
[2024-01-24 13:41:19,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900292075.1_PRJEB24954_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900292075.1_PRJEB24954_genomic.fna/checkm_input GCF_900292075.1_PRJEB24954_genomic.fna/checkm_result
[2024-01-24 13:42:26,226] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:26,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:26,242] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:26,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:26,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900292075.1_PRJEB24954_genomic.fna/markers.fasta)
[2024-01-24 13:42:26,242] [INFO] Task started: Blastn
[2024-01-24 13:42:26,243] [INFO] Running command: blastn -query GCF_900292075.1_PRJEB24954_genomic.fna/markers.fasta -db /var/lib/cwl/stg0787658e-e60b-4fae-ad49-b96b36556654/dqc_reference/reference_markers_gtdb.fasta -out GCF_900292075.1_PRJEB24954_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:28,030] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:28,032] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:28,032] [INFO] Target genome list was writen to GCF_900292075.1_PRJEB24954_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:28,040] [INFO] Task started: fastANI
[2024-01-24 13:42:28,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg2811b96a-359d-455a-b420-52e3a3fdaec3/GCF_900292075.1_PRJEB24954_genomic.fna.gz --refList GCF_900292075.1_PRJEB24954_genomic.fna/target_genomes_gtdb.txt --output GCF_900292075.1_PRJEB24954_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:41,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:41,198] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:41,198] [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_900292075.1	s__Microbacterium timonense	100.0	1315	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	83.9632	890	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	83.9246	907	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	83.8878	809	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	83.8671	850	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	83.8403	893	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	83.6242	908	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010634855.1	s__Microbacterium sp010634855	83.4627	868	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_009858275.1	s__Microbacterium sp009858275	83.4487	857	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278355.1	s__Microbacterium yannicii_B	83.2716	926	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	83.2586	857	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	83.1687	853	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	83.1377	840	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	83.0344	536	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,200] [INFO] GTDB search result was written to GCF_900292075.1_PRJEB24954_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:41,200] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:41,203] [INFO] DFAST_QC result json was written to GCF_900292075.1_PRJEB24954_genomic.fna/dqc_result.json
[2024-01-24 13:42:41,203] [INFO] DFAST_QC completed!
[2024-01-24 13:42:41,203] [INFO] Total running time: 0h1m46s