[2024-01-24 14:56:23,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference
[2024-01-24 14:56:26,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,558] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,558] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fd7720b-afb6-4dc2-ae81-fe53168c6729/GCF_030296555.1_ASM3029655v1_genomic.fna.gz | prodigal -d GCF_030296555.1_ASM3029655v1_genomic.fna/cds.fna -a GCF_030296555.1_ASM3029655v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:36,723] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:36,724] [INFO] Task started: HMMsearch
[2024-01-24 14:56:36,724] [INFO] Running command: hmmsearch --tblout GCF_030296555.1_ASM3029655v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference/reference_markers.hmm GCF_030296555.1_ASM3029655v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:37,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:37,052] [INFO] Found 6/6 markers.
[2024-01-24 14:56:37,102] [INFO] Query marker FASTA was written to GCF_030296555.1_ASM3029655v1_genomic.fna/markers.fasta
[2024-01-24 14:56:37,102] [INFO] Task started: Blastn
[2024-01-24 14:56:37,102] [INFO] Running command: blastn -query GCF_030296555.1_ASM3029655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference/reference_markers.fasta -out GCF_030296555.1_ASM3029655v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:38,351] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:38,363] [INFO] Selected 16 target genomes.
[2024-01-24 14:56:38,364] [INFO] Target genome list was writen to GCF_030296555.1_ASM3029655v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:38,378] [INFO] Task started: fastANI
[2024-01-24 14:56:38,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd7720b-afb6-4dc2-ae81-fe53168c6729/GCF_030296555.1_ASM3029655v1_genomic.fna.gz --refList GCF_030296555.1_ASM3029655v1_genomic.fna/target_genomes.txt --output GCF_030296555.1_ASM3029655v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:51,141] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:51,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:51,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:51,156] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:51,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:51,156] [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 commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	82.8432	615	1054	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	82.3646	608	1054	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.8963	625	1054	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	81.0144	547	1054	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	80.9818	561	1054	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	80.9299	493	1054	95	below_threshold
Microbacterium profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	80.7773	520	1054	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	80.6926	528	1054	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	80.686	483	1054	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	80.6669	533	1054	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	80.4307	487	1054	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8306	426	1054	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	79.7941	449	1054	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.634	482	1054	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.6299	423	1054	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.4412	381	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:51,161] [INFO] DFAST Taxonomy check result was written to GCF_030296555.1_ASM3029655v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:51,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:51,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:51,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference/checkm_data
[2024-01-24 14:56:51,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:51,200] [INFO] Task started: CheckM
[2024-01-24 14:56:51,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296555.1_ASM3029655v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296555.1_ASM3029655v1_genomic.fna/checkm_input GCF_030296555.1_ASM3029655v1_genomic.fna/checkm_result
[2024-01-24 14:57:35,773] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:35,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:35,797] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:35,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:35,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296555.1_ASM3029655v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:35,798] [INFO] Task started: Blastn
[2024-01-24 14:57:35,798] [INFO] Running command: blastn -query GCF_030296555.1_ASM3029655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ccef90-f131-4f22-98b4-96df4a611a7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296555.1_ASM3029655v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:37,669] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:37,674] [INFO] Selected 17 target genomes.
[2024-01-24 14:57:37,674] [INFO] Target genome list was writen to GCF_030296555.1_ASM3029655v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:37,692] [INFO] Task started: fastANI
[2024-01-24 14:57:37,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd7720b-afb6-4dc2-ae81-fe53168c6729/GCF_030296555.1_ASM3029655v1_genomic.fna.gz --refList GCF_030296555.1_ASM3029655v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296555.1_ASM3029655v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:50,653] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:50,668] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:57:50,668] [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
GCA_001897945.1	s__Microbacterium sp001897945	84.4003	688	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015040615.1	s__Microbacterium sp015040615	83.823	714	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	83.0261	607	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_001878835.1	s__Microbacterium sp001878835	82.7141	594	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.56	98.56	0.87	0.87	2	-
GCA_002837415.1	s__Microbacterium sp002837415	82.6403	591	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084045.1	s__Microbacterium esteraromaticum_D	82.4618	617	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907315.1	s__Microbacterium esteraromaticum	82.3836	609	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408055.1	s__Microbacterium esteraromaticum_C	82.0846	584	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.47	97.77	0.93	0.90	5	-
GCF_009758255.1	s__Microbacterium sp009758255	81.9653	623	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645325.1	s__Microbacterium sp903645325	81.0966	529	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988825.1	s__Microbacterium aerolatum	81.0023	548	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018268455.1	s__Microbacterium sp018268455	80.9652	462	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268515.1	s__Microbacterium sp018268515	80.6617	525	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017968845.1	s__Microbacterium sp017968845	80.4689	484	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898315.1	s__Microbacterium sp001898315	79.7654	398	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_014779795.1	s__Microbacterium helvum	79.6837	479	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009745985.1	s__Microbacterium karelineae	78.8509	363	1054	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 14:57:50,670] [INFO] GTDB search result was written to GCF_030296555.1_ASM3029655v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:50,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:50,675] [INFO] DFAST_QC result json was written to GCF_030296555.1_ASM3029655v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:50,675] [INFO] DFAST_QC completed!
[2024-01-24 14:57:50,675] [INFO] Total running time: 0h1m27s