[2024-01-24 11:12:39,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference
[2024-01-24 11:12:41,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,123] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,124] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfee14f6-82c1-4cf0-978c-27fc3c62b4ff/GCF_017876655.1_ASM1787665v1_genomic.fna.gz | prodigal -d GCF_017876655.1_ASM1787665v1_genomic.fna/cds.fna -a GCF_017876655.1_ASM1787665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,031] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,031] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,031] [INFO] Running command: hmmsearch --tblout GCF_017876655.1_ASM1787665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference/reference_markers.hmm GCF_017876655.1_ASM1787665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,287] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,318] [INFO] Query marker FASTA was written to GCF_017876655.1_ASM1787665v1_genomic.fna/markers.fasta
[2024-01-24 11:12:50,318] [INFO] Task started: Blastn
[2024-01-24 11:12:50,318] [INFO] Running command: blastn -query GCF_017876655.1_ASM1787665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference/reference_markers.fasta -out GCF_017876655.1_ASM1787665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,496] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,500] [INFO] Selected 22 target genomes.
[2024-01-24 11:12:51,500] [INFO] Target genome list was writen to GCF_017876655.1_ASM1787665v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,508] [INFO] Task started: fastANI
[2024-01-24 11:12:51,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfee14f6-82c1-4cf0-978c-27fc3c62b4ff/GCF_017876655.1_ASM1787665v1_genomic.fna.gz --refList GCF_017876655.1_ASM1787665v1_genomic.fna/target_genomes.txt --output GCF_017876655.1_ASM1787665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:07,079] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:07,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:07,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:07,096] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:07,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:07,097] [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 imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	100.0	1053	1054	95	conclusive
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	84.167	743	1054	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.7251	545	1054	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.614	582	1054	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.4705	539	1054	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.368	554	1054	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	81.248	564	1054	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.1778	524	1054	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	81.1592	530	1054	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	81.1299	581	1054	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	81.0831	527	1054	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	81.0291	543	1054	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.9906	513	1054	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.9624	547	1054	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.7386	545	1054	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	80.6934	539	1054	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	80.6819	540	1054	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.6687	565	1054	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.5408	519	1054	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.4561	543	1054	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	80.3685	524	1054	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	79.3581	397	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:07,099] [INFO] DFAST Taxonomy check result was written to GCF_017876655.1_ASM1787665v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:07,099] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:07,099] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:07,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference/checkm_data
[2024-01-24 11:13:07,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:07,140] [INFO] Task started: CheckM
[2024-01-24 11:13:07,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876655.1_ASM1787665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876655.1_ASM1787665v1_genomic.fna/checkm_input GCF_017876655.1_ASM1787665v1_genomic.fna/checkm_result
[2024-01-24 11:13:56,191] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:56,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:56,215] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:56,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:56,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876655.1_ASM1787665v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:56,216] [INFO] Task started: Blastn
[2024-01-24 11:13:56,217] [INFO] Running command: blastn -query GCF_017876655.1_ASM1787665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ac0583-6a5a-4a18-ae41-cdc9b6d98926/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876655.1_ASM1787665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:58,143] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:58,147] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:58,148] [INFO] Target genome list was writen to GCF_017876655.1_ASM1787665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:58,157] [INFO] Task started: fastANI
[2024-01-24 11:13:58,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfee14f6-82c1-4cf0-978c-27fc3c62b4ff/GCF_017876655.1_ASM1787665v1_genomic.fna.gz --refList GCF_017876655.1_ASM1787665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876655.1_ASM1787665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:04,973] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:04,988] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:04,989] [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_017876655.1	s__Microbacterium imperiale	100.0	1054	1054	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_002245215.1	s__Microbacterium sp002245215	85.7985	835	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_003289625.1	s__Microbacterium sp003289625	85.6399	791	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	-
GCF_003339645.1	s__Microbacterium arborescens	85.6194	810	1054	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_013389665.1	s__Microbacterium oleivorans_C	85.1747	774	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_003610405.1	s__Microbacterium sp003610405	85.1176	804	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_900102175.1	s__Microbacterium sp900102175	85.1169	771	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_003651225.1	s__Microbacterium telephonicum	81.5766	585	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 11:14:04,990] [INFO] GTDB search result was written to GCF_017876655.1_ASM1787665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:04,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:04,997] [INFO] DFAST_QC result json was written to GCF_017876655.1_ASM1787665v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:04,997] [INFO] DFAST_QC completed!
[2024-01-24 11:14:04,997] [INFO] Total running time: 0h1m25s