[2023-06-19 05:25:05,265] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:25:05,270] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:25:05,270] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference
[2023-06-19 05:25:07,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:25:07,576] [INFO] Task started: Prodigal
[2023-06-19 05:25:07,577] [INFO] Running command: gunzip -c /var/lib/cwl/stgeaeeba91-5a31-4d98-a5ba-b73acb139f63/GCA_018268515.1_ASM1826851v1_genomic.fna.gz | prodigal -d GCA_018268515.1_ASM1826851v1_genomic.fna/cds.fna -a GCA_018268515.1_ASM1826851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:25:17,461] [INFO] Task succeeded: Prodigal
[2023-06-19 05:25:17,462] [INFO] Task started: HMMsearch
[2023-06-19 05:25:17,462] [INFO] Running command: hmmsearch --tblout GCA_018268515.1_ASM1826851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference/reference_markers.hmm GCA_018268515.1_ASM1826851v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:25:17,719] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:25:17,721] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeaeeba91-5a31-4d98-a5ba-b73acb139f63/GCA_018268515.1_ASM1826851v1_genomic.fna.gz]
[2023-06-19 05:25:17,757] [INFO] Query marker FASTA was written to GCA_018268515.1_ASM1826851v1_genomic.fna/markers.fasta
[2023-06-19 05:25:17,758] [INFO] Task started: Blastn
[2023-06-19 05:25:17,758] [INFO] Running command: blastn -query GCA_018268515.1_ASM1826851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference/reference_markers.fasta -out GCA_018268515.1_ASM1826851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:18,659] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:18,666] [INFO] Selected 17 target genomes.
[2023-06-19 05:25:18,667] [INFO] Target genome list was writen to GCA_018268515.1_ASM1826851v1_genomic.fna/target_genomes.txt
[2023-06-19 05:25:18,672] [INFO] Task started: fastANI
[2023-06-19 05:25:18,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaeeba91-5a31-4d98-a5ba-b73acb139f63/GCA_018268515.1_ASM1826851v1_genomic.fna.gz --refList GCA_018268515.1_ASM1826851v1_genomic.fna/target_genomes.txt --output GCA_018268515.1_ASM1826851v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:30,421] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:30,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:30,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:30,438] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:30,438] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:25:30,438] [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 azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	85.864	806	1182	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.3998	606	1182	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	81.1081	581	1182	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.0367	533	1182	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	80.9042	497	1182	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	80.8544	493	1182	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	80.8502	550	1182	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	80.6867	520	1182	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	80.6797	509	1182	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	80.6059	514	1182	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	80.4129	542	1182	95	below_threshold
Microbacterium foliorum	strain=DSM 12966	GCA_000956415.1	104336	104336	suspected-type	True	80.3408	549	1182	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	79.9304	526	1182	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.7889	433	1182	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.5939	471	1182	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.5437	476	1182	95	below_threshold
Microbacterium protaetiae	strain=DFW100M-13	GCA_004135285.1	2509458	2509458	type	True	79.0723	416	1182	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:25:30,442] [INFO] DFAST Taxonomy check result was written to GCA_018268515.1_ASM1826851v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:30,443] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:30,443] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:30,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference/checkm_data
[2023-06-19 05:25:30,444] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:30,486] [INFO] Task started: CheckM
[2023-06-19 05:25:30,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018268515.1_ASM1826851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018268515.1_ASM1826851v1_genomic.fna/checkm_input GCA_018268515.1_ASM1826851v1_genomic.fna/checkm_result
[2023-06-19 05:26:18,759] [INFO] Task succeeded: CheckM
[2023-06-19 05:26:18,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:26:18,792] [INFO] ===== Completeness check finished =====
[2023-06-19 05:26:18,792] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:26:18,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018268515.1_ASM1826851v1_genomic.fna/markers.fasta)
[2023-06-19 05:26:18,794] [INFO] Task started: Blastn
[2023-06-19 05:26:18,794] [INFO] Running command: blastn -query GCA_018268515.1_ASM1826851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa56bb2a-0578-4f46-ab65-95c1232a8722/dqc_reference/reference_markers_gtdb.fasta -out GCA_018268515.1_ASM1826851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:26:20,248] [INFO] Task succeeded: Blastn
[2023-06-19 05:26:20,252] [INFO] Selected 10 target genomes.
[2023-06-19 05:26:20,252] [INFO] Target genome list was writen to GCA_018268515.1_ASM1826851v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:26:20,261] [INFO] Task started: fastANI
[2023-06-19 05:26:20,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaeeba91-5a31-4d98-a5ba-b73acb139f63/GCA_018268515.1_ASM1826851v1_genomic.fna.gz --refList GCA_018268515.1_ASM1826851v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018268515.1_ASM1826851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:26:28,885] [INFO] Task succeeded: fastANI
[2023-06-19 05:26:28,898] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:26:28,898] [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_018268515.1	s__Microbacterium sp018268515	100.0	1175	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002257455.1	s__Microbacterium sp002257455	88.0566	745	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956505.1	s__Microbacterium azadirachtae_A	87.788	858	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCA_017306305.1	s__Microbacterium sp017306305	86.55	816	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCA_018268435.1	s__Microbacterium sp018268435	86.3086	656	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956545.1	s__Microbacterium azadirachtae	85.8919	804	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	-
GCA_018268455.1	s__Microbacterium sp018268455	85.3588	714	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002837415.1	s__Microbacterium sp002837415	81.0956	535	1182	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	80.8692	496	1182	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	78.6789	420	1182	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:26:28,901] [INFO] GTDB search result was written to GCA_018268515.1_ASM1826851v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:26:28,901] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:26:28,905] [INFO] DFAST_QC result json was written to GCA_018268515.1_ASM1826851v1_genomic.fna/dqc_result.json
[2023-06-19 05:26:28,906] [INFO] DFAST_QC completed!
[2023-06-19 05:26:28,906] [INFO] Total running time: 0h1m24s