[2024-01-24 12:47:22,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference
[2024-01-24 12:47:23,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,444] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg723de11f-7ae0-4064-8739-7a384b96a89b/GCF_001456955.1_ASM145695v1_genomic.fna.gz | prodigal -d GCF_001456955.1_ASM145695v1_genomic.fna/cds.fna -a GCF_001456955.1_ASM145695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:33,912] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:33,912] [INFO] Task started: HMMsearch
[2024-01-24 12:47:33,913] [INFO] Running command: hmmsearch --tblout GCF_001456955.1_ASM145695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference/reference_markers.hmm GCF_001456955.1_ASM145695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:34,182] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:34,183] [INFO] Found 6/6 markers.
[2024-01-24 12:47:34,235] [INFO] Query marker FASTA was written to GCF_001456955.1_ASM145695v1_genomic.fna/markers.fasta
[2024-01-24 12:47:34,236] [INFO] Task started: Blastn
[2024-01-24 12:47:34,236] [INFO] Running command: blastn -query GCF_001456955.1_ASM145695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference/reference_markers.fasta -out GCF_001456955.1_ASM145695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:35,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:35,530] [INFO] Selected 12 target genomes.
[2024-01-24 12:47:35,531] [INFO] Target genome list was writen to GCF_001456955.1_ASM145695v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:35,536] [INFO] Task started: fastANI
[2024-01-24 12:47:35,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg723de11f-7ae0-4064-8739-7a384b96a89b/GCF_001456955.1_ASM145695v1_genomic.fna.gz --refList GCF_001456955.1_ASM145695v1_genomic.fna/target_genomes.txt --output GCF_001456955.1_ASM145695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:45,566] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:45,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:45,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:45,578] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:45,578] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:45,578] [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 enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	100.0	1214	1214	95	conclusive
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	100.0	1214	1214	95	conclusive
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	86.9415	920	1214	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	85.5664	815	1214	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.9968	532	1214	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.8775	499	1214	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	80.6606	535	1214	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.5725	549	1214	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.5283	559	1214	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.3666	572	1214	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.3562	551	1214	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.202	572	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:45,580] [INFO] DFAST Taxonomy check result was written to GCF_001456955.1_ASM145695v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:45,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:45,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:45,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference/checkm_data
[2024-01-24 12:47:45,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:45,629] [INFO] Task started: CheckM
[2024-01-24 12:47:45,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001456955.1_ASM145695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001456955.1_ASM145695v1_genomic.fna/checkm_input GCF_001456955.1_ASM145695v1_genomic.fna/checkm_result
[2024-01-24 12:48:27,902] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:27,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:27,926] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:27,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:27,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001456955.1_ASM145695v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:27,927] [INFO] Task started: Blastn
[2024-01-24 12:48:27,927] [INFO] Running command: blastn -query GCF_001456955.1_ASM145695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fad8a11-6910-44eb-a192-e467d6273c5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001456955.1_ASM145695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:29,797] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:29,803] [INFO] Selected 13 target genomes.
[2024-01-24 12:48:29,803] [INFO] Target genome list was writen to GCF_001456955.1_ASM145695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:29,840] [INFO] Task started: fastANI
[2024-01-24 12:48:29,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg723de11f-7ae0-4064-8739-7a384b96a89b/GCF_001456955.1_ASM145695v1_genomic.fna.gz --refList GCF_001456955.1_ASM145695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001456955.1_ASM145695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:40,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:40,866] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:40,866] [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_001456955.1	s__Microbacterium enclense	100.0	1214	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.78	97.57	0.95	0.89	3	conclusive
GCF_014192415.1	s__Microbacterium proteolyticum	86.9372	921	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424225.1	s__Microbacterium sp001424225	86.8817	928	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008763945.1	s__Microbacterium testaceum_G	86.2683	862	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004854025.1	s__Microbacterium hydrothermale	86.2043	852	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156435.1	s__Microbacterium sp900156435	85.9687	840	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007679045.1	s__Microbacterium sp007679045	85.9467	826	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCF_003075375.1	s__Microbacterium testaceum_E	85.9164	788	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.84	0.84	2	-
GCF_900104345.1	s__Microbacterium testaceum_A	85.8982	821	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.34	95.96	0.91	0.90	3	-
GCF_003386675.1	s__Microbacterium chocolatum_A	85.6524	846	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.92	0.92	2	-
GCF_017833635.1	s__Microbacterium sp017833635	85.5589	835	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476285.1	s__Microbacterium testaceum_B	85.064	769	1214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
GCA_016870695.1	s__Microbacterium sp016870695	84.1697	527	1214	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 12:48:40,868] [INFO] GTDB search result was written to GCF_001456955.1_ASM145695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:40,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:40,872] [INFO] DFAST_QC result json was written to GCF_001456955.1_ASM145695v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:40,872] [INFO] DFAST_QC completed!
[2024-01-24 12:48:40,872] [INFO] Total running time: 0h1m19s