[2024-01-25 20:21:20,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:20,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:20,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference
[2024-01-25 20:21:21,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:21,736] [INFO] Task started: Prodigal
[2024-01-25 20:21:21,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg26046889-4c3c-4a53-8a53-9dae60f7a9a3/GCF_030268005.1_ASM3026800v1_genomic.fna.gz | prodigal -d GCF_030268005.1_ASM3026800v1_genomic.fna/cds.fna -a GCF_030268005.1_ASM3026800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:31,176] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:31,177] [INFO] Task started: HMMsearch
[2024-01-25 20:21:31,177] [INFO] Running command: hmmsearch --tblout GCF_030268005.1_ASM3026800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference/reference_markers.hmm GCF_030268005.1_ASM3026800v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:31,385] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:31,386] [INFO] Found 6/6 markers.
[2024-01-25 20:21:31,417] [INFO] Query marker FASTA was written to GCF_030268005.1_ASM3026800v1_genomic.fna/markers.fasta
[2024-01-25 20:21:31,417] [INFO] Task started: Blastn
[2024-01-25 20:21:31,417] [INFO] Running command: blastn -query GCF_030268005.1_ASM3026800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference/reference_markers.fasta -out GCF_030268005.1_ASM3026800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:32,610] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:32,613] [INFO] Selected 17 target genomes.
[2024-01-25 20:21:32,613] [INFO] Target genome list was writen to GCF_030268005.1_ASM3026800v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:32,638] [INFO] Task started: fastANI
[2024-01-25 20:21:32,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg26046889-4c3c-4a53-8a53-9dae60f7a9a3/GCF_030268005.1_ASM3026800v1_genomic.fna.gz --refList GCF_030268005.1_ASM3026800v1_genomic.fna/target_genomes.txt --output GCF_030268005.1_ASM3026800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:44,911] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:44,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:44,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:44,923] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:21:44,923] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:21:44,923] [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 commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	83.2583	659	1220	95	below_threshold
Microbacterium esteraromaticum	strain=DSM 8609	GCA_016907315.1	57043	57043	suspected-type	True	82.8509	757	1220	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	82.7688	766	1220	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	81.5066	550	1220	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	81.3966	651	1220	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	81.3762	619	1220	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	81.3744	587	1220	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	81.2153	585	1220	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	81.2131	579	1220	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	81.1389	517	1220	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	80.9901	582	1220	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	80.9489	627	1220	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	80.9228	644	1220	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.8773	506	1220	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.8705	443	1220	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.6407	526	1220	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.5343	495	1220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:44,924] [INFO] DFAST Taxonomy check result was written to GCF_030268005.1_ASM3026800v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:44,925] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:44,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:44,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference/checkm_data
[2024-01-25 20:21:44,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:44,976] [INFO] Task started: CheckM
[2024-01-25 20:21:44,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030268005.1_ASM3026800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030268005.1_ASM3026800v1_genomic.fna/checkm_input GCF_030268005.1_ASM3026800v1_genomic.fna/checkm_result
[2024-01-25 20:22:51,218] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:51,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:51,243] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:51,243] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:51,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030268005.1_ASM3026800v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:51,244] [INFO] Task started: Blastn
[2024-01-25 20:22:51,245] [INFO] Running command: blastn -query GCF_030268005.1_ASM3026800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f6d9639-c252-4fac-9e3f-31e9a9f3d5df/dqc_reference/reference_markers_gtdb.fasta -out GCF_030268005.1_ASM3026800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:53,249] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:53,253] [INFO] Selected 7 target genomes.
[2024-01-25 20:22:53,253] [INFO] Target genome list was writen to GCF_030268005.1_ASM3026800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:53,263] [INFO] Task started: fastANI
[2024-01-25 20:22:53,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg26046889-4c3c-4a53-8a53-9dae60f7a9a3/GCF_030268005.1_ASM3026800v1_genomic.fna.gz --refList GCF_030268005.1_ASM3026800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030268005.1_ASM3026800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:58,771] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:58,777] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:22:58,778] [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_001897945.1	s__Microbacterium sp001897945	93.7983	923	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015040615.1	s__Microbacterium sp015040615	84.3014	796	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705755.3	s__Microbacterium esteraromaticum_A	83.3546	693	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.15	98.15	0.64	0.64	2	-
GCF_001878835.1	s__Microbacterium sp001878835	83.2096	638	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.56	98.56	0.87	0.87	2	-
GCA_002837415.1	s__Microbacterium sp002837415	83.1645	648	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014084045.1	s__Microbacterium esteraromaticum_D	82.9932	722	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907315.1	s__Microbacterium esteraromaticum	82.8728	755	1220	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:58,779] [INFO] GTDB search result was written to GCF_030268005.1_ASM3026800v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:58,779] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:58,782] [INFO] DFAST_QC result json was written to GCF_030268005.1_ASM3026800v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:58,783] [INFO] DFAST_QC completed!
[2024-01-25 20:22:58,783] [INFO] Total running time: 0h1m38s