[2024-01-24 10:57:38,591] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,594] [INFO] DQC Reference Directory: /var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference
[2024-01-24 10:57:39,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,956] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,956] [INFO] Running command: gunzip -c /var/lib/cwl/stgd79e4bc5-6279-47fc-93dd-9974b617417d/GCF_023155855.1_ASM2315585v1_genomic.fna.gz | prodigal -d GCF_023155855.1_ASM2315585v1_genomic.fna/cds.fna -a GCF_023155855.1_ASM2315585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:51,088] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:51,089] [INFO] Task started: HMMsearch
[2024-01-24 10:57:51,089] [INFO] Running command: hmmsearch --tblout GCF_023155855.1_ASM2315585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference/reference_markers.hmm GCF_023155855.1_ASM2315585v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:51,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:51,356] [INFO] Found 6/6 markers.
[2024-01-24 10:57:51,392] [INFO] Query marker FASTA was written to GCF_023155855.1_ASM2315585v1_genomic.fna/markers.fasta
[2024-01-24 10:57:51,392] [INFO] Task started: Blastn
[2024-01-24 10:57:51,392] [INFO] Running command: blastn -query GCF_023155855.1_ASM2315585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference/reference_markers.fasta -out GCF_023155855.1_ASM2315585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:52,547] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:52,550] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:52,550] [INFO] Target genome list was writen to GCF_023155855.1_ASM2315585v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:52,559] [INFO] Task started: fastANI
[2024-01-24 10:57:52,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgd79e4bc5-6279-47fc-93dd-9974b617417d/GCF_023155855.1_ASM2315585v1_genomic.fna.gz --refList GCF_023155855.1_ASM2315585v1_genomic.fna/target_genomes.txt --output GCF_023155855.1_ASM2315585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:08,652] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:08,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:08,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:08,675] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:08,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:08,675] [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 gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.1071	665	1292	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	82.0979	622	1292	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	82.0503	667	1292	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	81.9728	628	1292	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	81.9399	722	1292	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	81.9316	672	1292	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	81.9035	699	1292	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	81.8851	694	1292	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	81.8372	685	1292	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	81.6742	706	1292	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	81.3895	656	1292	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	81.295	706	1292	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.1924	558	1292	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.1287	573	1292	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.0816	564	1292	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	81.0708	608	1292	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.0621	546	1292	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	80.5869	538	1292	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	80.5554	528	1292	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	80.3514	517	1292	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	80.0829	444	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:08,677] [INFO] DFAST Taxonomy check result was written to GCF_023155855.1_ASM2315585v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:08,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:08,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:08,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference/checkm_data
[2024-01-24 10:58:08,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:08,716] [INFO] Task started: CheckM
[2024-01-24 10:58:08,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023155855.1_ASM2315585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023155855.1_ASM2315585v1_genomic.fna/checkm_input GCF_023155855.1_ASM2315585v1_genomic.fna/checkm_result
[2024-01-24 10:59:06,218] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:06,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:06,247] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:06,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:06,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023155855.1_ASM2315585v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:06,248] [INFO] Task started: Blastn
[2024-01-24 10:59:06,248] [INFO] Running command: blastn -query GCF_023155855.1_ASM2315585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge371b7ae-5a7f-4480-9bf8-c6d50518d012/dqc_reference/reference_markers_gtdb.fasta -out GCF_023155855.1_ASM2315585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:08,258] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:08,262] [INFO] Selected 26 target genomes.
[2024-01-24 10:59:08,262] [INFO] Target genome list was writen to GCF_023155855.1_ASM2315585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:08,281] [INFO] Task started: fastANI
[2024-01-24 10:59:08,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgd79e4bc5-6279-47fc-93dd-9974b617417d/GCF_023155855.1_ASM2315585v1_genomic.fna.gz --refList GCF_023155855.1_ASM2315585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023155855.1_ASM2315585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:29,240] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:29,263] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:59:29,263] [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_014837165.1	s__Microbacterium sp014837165	82.0959	666	1292	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	82.0451	668	1292	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	82.0012	649	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005502885.1	s__Microbacterium sp005502885	81.9963	702	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428485.1	s__Microbacterium sp001428485	81.9721	684	1292	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	81.9704	719	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	81.9529	727	1292	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	81.9521	699	1292	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	81.9222	696	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	81.9213	673	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	81.897	703	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858275.1	s__Microbacterium sp009858275	81.886	704	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	81.861	696	1292	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	81.7553	650	1292	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	81.7116	702	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900155915.1	s__Microbacterium sp900155915	81.6322	666	1292	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	81.6103	668	1292	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	81.2543	686	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991875.1	s__Microbacterium lemovicicum	81.0459	610	1292	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	80.8715	667	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427525.1	s__Microbacterium sp001427525	80.8527	620	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710705.1	s__Microbacterium radiodurans	80.6553	532	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000202635.1	s__Microbacterium testaceum_F	80.3902	557	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691565.1	s__Microbacterium oleivorans_B	80.3028	494	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306415.1	s__Microbacterium sp001897105	80.2295	561	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.03	95.75	0.95	0.85	5	-
GCF_001652465.1	s__Microbacterium chocolatum	80.196	566	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.91	96.78	0.87	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:29,265] [INFO] GTDB search result was written to GCF_023155855.1_ASM2315585v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:29,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:29,270] [INFO] DFAST_QC result json was written to GCF_023155855.1_ASM2315585v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:29,270] [INFO] DFAST_QC completed!
[2024-01-24 10:59:29,270] [INFO] Total running time: 0h1m51s