[2024-01-24 11:12:36,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference
[2024-01-24 11:12:38,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,662] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,662] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbb7773f-8601-498b-ad68-bea186ec7324/GCF_017876435.1_ASM1787643v1_genomic.fna.gz | prodigal -d GCF_017876435.1_ASM1787643v1_genomic.fna/cds.fna -a GCF_017876435.1_ASM1787643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,171] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,171] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,171] [INFO] Running command: hmmsearch --tblout GCF_017876435.1_ASM1787643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference/reference_markers.hmm GCF_017876435.1_ASM1787643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,385] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,386] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,419] [INFO] Query marker FASTA was written to GCF_017876435.1_ASM1787643v1_genomic.fna/markers.fasta
[2024-01-24 11:12:50,419] [INFO] Task started: Blastn
[2024-01-24 11:12:50,419] [INFO] Running command: blastn -query GCF_017876435.1_ASM1787643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference/reference_markers.fasta -out GCF_017876435.1_ASM1787643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,479] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,482] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:51,482] [INFO] Target genome list was writen to GCF_017876435.1_ASM1787643v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,493] [INFO] Task started: fastANI
[2024-01-24 11:12:51,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb7773f-8601-498b-ad68-bea186ec7324/GCF_017876435.1_ASM1787643v1_genomic.fna.gz --refList GCF_017876435.1_ASM1787643v1_genomic.fna/target_genomes.txt --output GCF_017876435.1_ASM1787643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:01,425] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:01,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:01,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:01,436] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:01,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:01,436] [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 phyllosphaerae	strain=DSM 13468	GCA_017876435.1	124798	124798	type	True	100.0	1242	1242	95	conclusive
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	86.1264	885	1242	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	86.0918	930	1242	95	below_threshold
Microbacterium foliorum	strain=DSM 12966	GCA_000956415.1	104336	104336	suspected-type	True	86.0848	878	1242	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	86.0801	883	1242	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	83.273	734	1242	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	83.2681	737	1242	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	83.1663	791	1242	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.2314	568	1242	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.0328	618	1242	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.006	502	1242	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.5569	458	1242	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.5041	490	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:01,438] [INFO] DFAST Taxonomy check result was written to GCF_017876435.1_ASM1787643v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:01,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:01,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:01,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference/checkm_data
[2024-01-24 11:13:01,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:01,476] [INFO] Task started: CheckM
[2024-01-24 11:13:01,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876435.1_ASM1787643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876435.1_ASM1787643v1_genomic.fna/checkm_input GCF_017876435.1_ASM1787643v1_genomic.fna/checkm_result
[2024-01-24 11:14:15,952] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:15,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:15,969] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:15,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:15,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876435.1_ASM1787643v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:15,970] [INFO] Task started: Blastn
[2024-01-24 11:14:15,970] [INFO] Running command: blastn -query GCF_017876435.1_ASM1787643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fa9326f-32d8-44d9-82c9-d7d235103167/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876435.1_ASM1787643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:17,748] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:17,751] [INFO] Selected 11 target genomes.
[2024-01-24 11:14:17,751] [INFO] Target genome list was writen to GCF_017876435.1_ASM1787643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:17,759] [INFO] Task started: fastANI
[2024-01-24 11:14:17,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbb7773f-8601-498b-ad68-bea186ec7324/GCF_017876435.1_ASM1787643v1_genomic.fna.gz --refList GCF_017876435.1_ASM1787643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876435.1_ASM1787643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:28,234] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:28,243] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:28,244] [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_017876435.1	s__Microbacterium phyllosphaerae	100.0	1241	1242	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_001423615.1	s__Microbacterium sp001423615	89.7987	1032	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.40	98.40	0.90	0.90	2	-
GCF_001423485.1	s__Microbacterium sp001423485	89.4049	1006	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002024885.1	s__Microbacterium foliorum_A	87.1972	969	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	97.34	0.94	0.92	3	-
GCF_018613995.1	s__Microbacterium sp018613995	87.1707	687	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889265.1	s__Microbacterium sp001889265	86.9294	921	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.81	98.68	0.92	0.91	4	-
GCF_015354505.1	s__Microbacterium sp015354505	86.8384	906	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385575.1	s__Microbacterium foliorum_B	86.8283	933	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426995.1	s__Microbacterium sp001426995	86.2953	903	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.85	97.85	0.92	0.92	2	-
GCF_003367705.1	s__Microbacterium foliorum	86.1283	887	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904831005.1	s__Microbacterium hydrocarbonoxydans_B	85.399	890	1242	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 11:14:28,245] [INFO] GTDB search result was written to GCF_017876435.1_ASM1787643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:28,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:28,249] [INFO] DFAST_QC result json was written to GCF_017876435.1_ASM1787643v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:28,249] [INFO] DFAST_QC completed!
[2024-01-24 11:14:28,249] [INFO] Total running time: 0h1m52s