[2024-01-24 10:47:23,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:23,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:23,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference
[2024-01-24 10:47:26,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,182] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7f4196f-5a92-490c-97f8-b84420199133/GCF_014640975.1_ASM1464097v1_genomic.fna.gz | prodigal -d GCF_014640975.1_ASM1464097v1_genomic.fna/cds.fna -a GCF_014640975.1_ASM1464097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:35,220] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:35,221] [INFO] Task started: HMMsearch
[2024-01-24 10:47:35,221] [INFO] Running command: hmmsearch --tblout GCF_014640975.1_ASM1464097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference/reference_markers.hmm GCF_014640975.1_ASM1464097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:35,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:35,514] [INFO] Found 6/6 markers.
[2024-01-24 10:47:35,543] [INFO] Query marker FASTA was written to GCF_014640975.1_ASM1464097v1_genomic.fna/markers.fasta
[2024-01-24 10:47:35,544] [INFO] Task started: Blastn
[2024-01-24 10:47:35,544] [INFO] Running command: blastn -query GCF_014640975.1_ASM1464097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference/reference_markers.fasta -out GCF_014640975.1_ASM1464097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:36,582] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:36,586] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:36,586] [INFO] Target genome list was writen to GCF_014640975.1_ASM1464097v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:36,609] [INFO] Task started: fastANI
[2024-01-24 10:47:36,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7f4196f-5a92-490c-97f8-b84420199133/GCF_014640975.1_ASM1464097v1_genomic.fna.gz --refList GCF_014640975.1_ASM1464097v1_genomic.fna/target_genomes.txt --output GCF_014640975.1_ASM1464097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:45,605] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:45,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:45,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:45,617] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:45,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:45,617] [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 faecale	strain=CGMCC 1.15152	GCA_014640975.1	1804630	1804630	type	True	100.0	1038	1038	95	conclusive
Microbacterium gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	81.5439	527	1038	95	below_threshold
Microbacterium suaedae	strain=YZYP 306	GCA_003254645.1	2067813	2067813	type	True	80.955	528	1038	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	80.6793	497	1038	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	80.6583	513	1038	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	80.6365	461	1038	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	80.4696	466	1038	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	80.3601	496	1038	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.2948	405	1038	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	78.9597	318	1038	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	78.6365	359	1038	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	78.5578	372	1038	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.4751	334	1038	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.2978	364	1038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:45,619] [INFO] DFAST Taxonomy check result was written to GCF_014640975.1_ASM1464097v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:45,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:45,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:45,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference/checkm_data
[2024-01-24 10:47:45,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:45,654] [INFO] Task started: CheckM
[2024-01-24 10:47:45,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640975.1_ASM1464097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640975.1_ASM1464097v1_genomic.fna/checkm_input GCF_014640975.1_ASM1464097v1_genomic.fna/checkm_result
[2024-01-24 10:48:20,239] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:20,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,265] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:20,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:20,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640975.1_ASM1464097v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:20,267] [INFO] Task started: Blastn
[2024-01-24 10:48:20,267] [INFO] Running command: blastn -query GCF_014640975.1_ASM1464097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42ff2bb6-833d-4d16-8dce-3a732597314e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640975.1_ASM1464097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:21,884] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:21,888] [INFO] Selected 10 target genomes.
[2024-01-24 10:48:21,888] [INFO] Target genome list was writen to GCF_014640975.1_ASM1464097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:21,917] [INFO] Task started: fastANI
[2024-01-24 10:48:21,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7f4196f-5a92-490c-97f8-b84420199133/GCF_014640975.1_ASM1464097v1_genomic.fna.gz --refList GCF_014640975.1_ASM1464097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640975.1_ASM1464097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:29,092] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:29,106] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:29,106] [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_014640975.1	s__Microbacterium faecale	100.0	1038	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.13	95.13	0.92	0.92	2	conclusive
GCF_000422745.1	s__Microbacterium gubbeenense	81.535	528	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117025.1	s__Microbacterium stercoravium	81.4358	467	1038	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	81.3567	598	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254645.1	s__Microbacterium suaedae	80.9738	527	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	80.6348	515	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	80.6089	463	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_014646015.1	s__Microbacterium nanhaiense	80.3718	495	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	78.5903	344	1038	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900078385.1	s__Microbacterium sp900078385	78.2379	353	1038	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 10:48:29,108] [INFO] GTDB search result was written to GCF_014640975.1_ASM1464097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:29,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:29,111] [INFO] DFAST_QC result json was written to GCF_014640975.1_ASM1464097v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:29,112] [INFO] DFAST_QC completed!
[2024-01-24 10:48:29,112] [INFO] Total running time: 0h1m6s