[2024-01-25 18:09:20,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:20,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:20,483] [INFO] DQC Reference Directory: /var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference
[2024-01-25 18:09:21,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:21,589] [INFO] Task started: Prodigal
[2024-01-25 18:09:21,589] [INFO] Running command: gunzip -c /var/lib/cwl/stge9728983-b05f-4b6c-b2fb-59995deddaa7/GCF_018588945.1_ASM1858894v1_genomic.fna.gz | prodigal -d GCF_018588945.1_ASM1858894v1_genomic.fna/cds.fna -a GCF_018588945.1_ASM1858894v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:30,188] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:30,188] [INFO] Task started: HMMsearch
[2024-01-25 18:09:30,189] [INFO] Running command: hmmsearch --tblout GCF_018588945.1_ASM1858894v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference/reference_markers.hmm GCF_018588945.1_ASM1858894v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:30,388] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:30,390] [INFO] Found 6/6 markers.
[2024-01-25 18:09:30,421] [INFO] Query marker FASTA was written to GCF_018588945.1_ASM1858894v1_genomic.fna/markers.fasta
[2024-01-25 18:09:30,421] [INFO] Task started: Blastn
[2024-01-25 18:09:30,421] [INFO] Running command: blastn -query GCF_018588945.1_ASM1858894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference/reference_markers.fasta -out GCF_018588945.1_ASM1858894v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:31,509] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:31,512] [INFO] Selected 14 target genomes.
[2024-01-25 18:09:31,512] [INFO] Target genome list was writen to GCF_018588945.1_ASM1858894v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:31,533] [INFO] Task started: fastANI
[2024-01-25 18:09:31,533] [INFO] Running command: fastANI --query /var/lib/cwl/stge9728983-b05f-4b6c-b2fb-59995deddaa7/GCF_018588945.1_ASM1858894v1_genomic.fna.gz --refList GCF_018588945.1_ASM1858894v1_genomic.fna/target_genomes.txt --output GCF_018588945.1_ASM1858894v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:43,122] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:43,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:43,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:43,131] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:43,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:43,132] [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 flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	100.0	1130	1131	95	conclusive
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	87.693	931	1131	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	85.263	855	1131	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	83.1981	745	1131	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	82.995	740	1131	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	82.9669	754	1131	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	82.6875	713	1131	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	82.6105	718	1131	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	82.4561	734	1131	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	81.7444	615	1131	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.367	553	1131	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.0627	537	1131	95	below_threshold
Microbacterium azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	80.2271	499	1131	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	80.1283	521	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:43,135] [INFO] DFAST Taxonomy check result was written to GCF_018588945.1_ASM1858894v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:43,137] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:43,137] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:43,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference/checkm_data
[2024-01-25 18:09:43,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:43,174] [INFO] Task started: CheckM
[2024-01-25 18:09:43,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018588945.1_ASM1858894v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018588945.1_ASM1858894v1_genomic.fna/checkm_input GCF_018588945.1_ASM1858894v1_genomic.fna/checkm_result
[2024-01-25 18:10:30,814] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:30,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:30,840] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:30,840] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:30,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018588945.1_ASM1858894v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:30,841] [INFO] Task started: Blastn
[2024-01-25 18:10:30,841] [INFO] Running command: blastn -query GCF_018588945.1_ASM1858894v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee179756-3375-4aec-bc0d-77dbece21fba/dqc_reference/reference_markers_gtdb.fasta -out GCF_018588945.1_ASM1858894v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:32,666] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:32,669] [INFO] Selected 14 target genomes.
[2024-01-25 18:10:32,669] [INFO] Target genome list was writen to GCF_018588945.1_ASM1858894v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:32,686] [INFO] Task started: fastANI
[2024-01-25 18:10:32,686] [INFO] Running command: fastANI --query /var/lib/cwl/stge9728983-b05f-4b6c-b2fb-59995deddaa7/GCF_018588945.1_ASM1858894v1_genomic.fna.gz --refList GCF_018588945.1_ASM1858894v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018588945.1_ASM1858894v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:44,809] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:44,818] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:44,818] [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_018588945.1	s__Microbacterium flavescens	100.0	1130	1131	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_014837165.1	s__Microbacterium sp014837165	87.7072	930	1131	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	85.2534	856	1131	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	84.1689	761	1131	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	84.0873	764	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012847295.1	s__Microbacterium sp012847295	83.7016	777	1131	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907635.1	s__Microbacterium insulae	83.4745	751	1131	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	83.1667	748	1131	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	83.0753	498	1131	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	82.9896	741	1131	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	82.9626	755	1131	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	82.696	712	1131	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	82.5633	706	1131	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	82.2671	705	1131	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 18:10:44,820] [INFO] GTDB search result was written to GCF_018588945.1_ASM1858894v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:44,820] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:44,824] [INFO] DFAST_QC result json was written to GCF_018588945.1_ASM1858894v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:44,825] [INFO] DFAST_QC completed!
[2024-01-25 18:10:44,825] [INFO] Total running time: 0h1m24s