[2024-01-24 13:18:41,850] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference
[2024-01-24 13:18:43,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:43,261] [INFO] Task started: Prodigal
[2024-01-24 13:18:43,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e86d625-b716-4543-b73e-07b2d6c45f38/GCF_013004565.1_ASM1300456v1_genomic.fna.gz | prodigal -d GCF_013004565.1_ASM1300456v1_genomic.fna/cds.fna -a GCF_013004565.1_ASM1300456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:52,636] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:52,636] [INFO] Task started: HMMsearch
[2024-01-24 13:18:52,637] [INFO] Running command: hmmsearch --tblout GCF_013004565.1_ASM1300456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference/reference_markers.hmm GCF_013004565.1_ASM1300456v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:52,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:52,913] [INFO] Found 6/6 markers.
[2024-01-24 13:18:52,951] [INFO] Query marker FASTA was written to GCF_013004565.1_ASM1300456v1_genomic.fna/markers.fasta
[2024-01-24 13:18:52,952] [INFO] Task started: Blastn
[2024-01-24 13:18:52,952] [INFO] Running command: blastn -query GCF_013004565.1_ASM1300456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference/reference_markers.fasta -out GCF_013004565.1_ASM1300456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:54,210] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:54,214] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:54,215] [INFO] Target genome list was writen to GCF_013004565.1_ASM1300456v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:54,227] [INFO] Task started: fastANI
[2024-01-24 13:18:54,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e86d625-b716-4543-b73e-07b2d6c45f38/GCF_013004565.1_ASM1300456v1_genomic.fna.gz --refList GCF_013004565.1_ASM1300456v1_genomic.fna/target_genomes.txt --output GCF_013004565.1_ASM1300456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:06,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:06,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:06,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:06,160] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:06,160] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:06,160] [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 ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	100.0	1131	1135	95	conclusive
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	99.9966	1133	1135	95	conclusive
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.7539	613	1135	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	81.7379	624	1135	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	81.6489	641	1135	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	81.6131	648	1135	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	81.5821	662	1135	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	81.5308	675	1135	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	81.4798	635	1135	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	81.1307	626	1135	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.1138	544	1135	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	81.0461	654	1135	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.7228	549	1135	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.5308	552	1135	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	80.44	531	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:06,162] [INFO] DFAST Taxonomy check result was written to GCF_013004565.1_ASM1300456v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:06,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:06,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:06,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference/checkm_data
[2024-01-24 13:19:06,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:06,199] [INFO] Task started: CheckM
[2024-01-24 13:19:06,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013004565.1_ASM1300456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013004565.1_ASM1300456v1_genomic.fna/checkm_input GCF_013004565.1_ASM1300456v1_genomic.fna/checkm_result
[2024-01-24 13:19:51,654] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:51,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:51,673] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:51,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:51,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013004565.1_ASM1300456v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:51,674] [INFO] Task started: Blastn
[2024-01-24 13:19:51,674] [INFO] Running command: blastn -query GCF_013004565.1_ASM1300456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg770da874-a0fa-411c-bf57-32e989e43cb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013004565.1_ASM1300456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:53,662] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:53,667] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:53,668] [INFO] Target genome list was writen to GCF_013004565.1_ASM1300456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:53,719] [INFO] Task started: fastANI
[2024-01-24 13:19:53,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e86d625-b716-4543-b73e-07b2d6c45f38/GCF_013004565.1_ASM1300456v1_genomic.fna.gz --refList GCF_013004565.1_ASM1300456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013004565.1_ASM1300456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:11,593] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:11,622] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:11,623] [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_011759705.1	s__Microbacterium ulmi	99.9966	1133	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900155915.1	s__Microbacterium sp900155915	82.1635	662	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046485.1	s__Microbacterium sp011046485	81.9621	648	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715675.1	s__Microbacterium sp006715675	81.8653	669	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	81.7932	660	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999995.1	s__Microbacterium sp003999995	81.7045	627	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	81.6933	435	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	81.6482	641	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	81.6296	658	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	81.6279	646	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	81.5765	605	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	81.531	675	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_004362195.1	s__Microbacterium sp004362195	81.4574	633	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	81.4237	649	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907635.1	s__Microbacterium insulae	81.3914	609	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010634855.1	s__Microbacterium sp010634855	81.3644	651	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_000380605.1	s__Microbacterium sp000380605	81.2441	675	1135	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	81.1512	542	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408285.1	s__Microbacterium sp013408285	81.1454	624	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114345.1	s__Microbacterium sp900114345	80.9719	589	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592125.1	s__Microbacterium hominis	80.7062	551	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.42	0.92	0.89	6	-
GCF_007828185.1	s__Microbacterium sp007828185	80.3549	534	1135	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 13:20:11,625] [INFO] GTDB search result was written to GCF_013004565.1_ASM1300456v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:11,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:11,632] [INFO] DFAST_QC result json was written to GCF_013004565.1_ASM1300456v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:11,632] [INFO] DFAST_QC completed!
[2024-01-24 13:20:11,632] [INFO] Total running time: 0h1m30s