[2024-01-24 13:13:38,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:38,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:38,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference
[2024-01-24 13:13:39,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:39,617] [INFO] Task started: Prodigal
[2024-01-24 13:13:39,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg42c474f3-133e-44ec-9431-20acc7c7edb5/GCF_008710745.1_ASM871074v1_genomic.fna.gz | prodigal -d GCF_008710745.1_ASM871074v1_genomic.fna/cds.fna -a GCF_008710745.1_ASM871074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:53,732] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:53,733] [INFO] Task started: HMMsearch
[2024-01-24 13:13:53,733] [INFO] Running command: hmmsearch --tblout GCF_008710745.1_ASM871074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference/reference_markers.hmm GCF_008710745.1_ASM871074v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:53,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:53,998] [INFO] Found 6/6 markers.
[2024-01-24 13:13:54,044] [INFO] Query marker FASTA was written to GCF_008710745.1_ASM871074v1_genomic.fna/markers.fasta
[2024-01-24 13:13:54,044] [INFO] Task started: Blastn
[2024-01-24 13:13:54,044] [INFO] Running command: blastn -query GCF_008710745.1_ASM871074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference/reference_markers.fasta -out GCF_008710745.1_ASM871074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:55,232] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:55,236] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:55,237] [INFO] Target genome list was writen to GCF_008710745.1_ASM871074v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:55,244] [INFO] Task started: fastANI
[2024-01-24 13:13:55,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c474f3-133e-44ec-9431-20acc7c7edb5/GCF_008710745.1_ASM871074v1_genomic.fna.gz --refList GCF_008710745.1_ASM871074v1_genomic.fna/target_genomes.txt --output GCF_008710745.1_ASM871074v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:09,288] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:09,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:09,305] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:09,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:09,306] [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 rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	100.0	1395	1396	95	conclusive
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	80.5283	663	1396	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.3993	580	1396	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.2801	605	1396	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.2799	600	1396	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.2646	591	1396	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.211	629	1396	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.1403	610	1396	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.131	572	1396	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.1024	567	1396	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.1004	564	1396	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.005	618	1396	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	79.8899	572	1396	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	79.7982	488	1396	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	79.7745	483	1396	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	79.7205	521	1396	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	78.8849	370	1396	95	below_threshold
Microbacterium protaetiae	strain=DFW100M-13	GCA_004135285.1	2509458	2509458	type	True	78.7703	437	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,308] [INFO] DFAST Taxonomy check result was written to GCF_008710745.1_ASM871074v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:09,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:09,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:09,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference/checkm_data
[2024-01-24 13:14:09,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:09,353] [INFO] Task started: CheckM
[2024-01-24 13:14:09,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008710745.1_ASM871074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008710745.1_ASM871074v1_genomic.fna/checkm_input GCF_008710745.1_ASM871074v1_genomic.fna/checkm_result
[2024-01-24 13:14:55,593] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:55,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:55,613] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:55,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:55,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008710745.1_ASM871074v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:55,614] [INFO] Task started: Blastn
[2024-01-24 13:14:55,614] [INFO] Running command: blastn -query GCF_008710745.1_ASM871074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg503cf426-84c0-4313-8675-c8b71cb1ceda/dqc_reference/reference_markers_gtdb.fasta -out GCF_008710745.1_ASM871074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:57,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:57,445] [INFO] Selected 24 target genomes.
[2024-01-24 13:14:57,445] [INFO] Target genome list was writen to GCF_008710745.1_ASM871074v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:57,481] [INFO] Task started: fastANI
[2024-01-24 13:14:57,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg42c474f3-133e-44ec-9431-20acc7c7edb5/GCF_008710745.1_ASM871074v1_genomic.fna.gz --refList GCF_008710745.1_ASM871074v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008710745.1_ASM871074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:16,077] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:16,096] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:16,097] [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_008710745.1	s__Microbacterium rhizomatis	100.0	1395	1396	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_001427525.1	s__Microbacterium sp001427525	80.5881	618	1396	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	80.5459	661	1396	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	80.4449	612	1396	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	80.3711	624	1396	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	80.3094	597	1396	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	80.3073	570	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837165.1	s__Microbacterium sp014837165	80.2672	590	1396	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	80.2199	628	1396	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	80.2136	641	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931875.1	s__Microbacterium sp003931875	80.1874	573	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	80.1873	583	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013409015.1	s__Microbacterium sp013409015	80.1839	614	1396	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	80.1572	633	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	80.1311	611	1396	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	80.1309	572	1396	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	80.1025	569	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620715.1	s__Microbacterium sp011620715	80.0969	456	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248655.1	s__Microbacterium sp003248655	80.0635	477	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000304335.1	s__Microbacterium yannicii_A	79.9693	563	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278355.1	s__Microbacterium yannicii_B	79.9041	628	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	79.8974	521	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812725.1	s__Microbacterium sp002812725	79.8776	502	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.24	99.24	0.94	0.94	2	-
GCF_012524205.1	s__Microbacterium sp012524205	79.825	579	1396	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 13:15:16,098] [INFO] GTDB search result was written to GCF_008710745.1_ASM871074v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:16,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:16,106] [INFO] DFAST_QC result json was written to GCF_008710745.1_ASM871074v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:16,107] [INFO] DFAST_QC completed!
[2024-01-24 13:15:16,107] [INFO] Total running time: 0h1m38s