[2024-01-24 10:47:09,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference
[2024-01-24 10:47:11,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,941] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a9ea9fc-7516-42f1-bbe2-f798a1514f54/GCF_014205075.1_ASM1420507v1_genomic.fna.gz | prodigal -d GCF_014205075.1_ASM1420507v1_genomic.fna/cds.fna -a GCF_014205075.1_ASM1420507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,065] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,065] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,065] [INFO] Running command: hmmsearch --tblout GCF_014205075.1_ASM1420507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference/reference_markers.hmm GCF_014205075.1_ASM1420507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,321] [INFO] Found 6/6 markers.
[2024-01-24 10:47:21,350] [INFO] Query marker FASTA was written to GCF_014205075.1_ASM1420507v1_genomic.fna/markers.fasta
[2024-01-24 10:47:21,351] [INFO] Task started: Blastn
[2024-01-24 10:47:21,351] [INFO] Running command: blastn -query GCF_014205075.1_ASM1420507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference/reference_markers.fasta -out GCF_014205075.1_ASM1420507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,517] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,529] [INFO] Selected 13 target genomes.
[2024-01-24 10:47:22,530] [INFO] Target genome list was writen to GCF_014205075.1_ASM1420507v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,479] [INFO] Task started: fastANI
[2024-01-24 10:47:23,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a9ea9fc-7516-42f1-bbe2-f798a1514f54/GCF_014205075.1_ASM1420507v1_genomic.fna.gz --refList GCF_014205075.1_ASM1420507v1_genomic.fna/target_genomes.txt --output GCF_014205075.1_ASM1420507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:32,887] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:32,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:32,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:32,899] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:32,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:32,899] [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 ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	100.0	1012	1012	95	conclusive
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	99.9947	1006	1012	95	conclusive
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	83.936	686	1012	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	83.8223	689	1012	95	below_threshold
Microbacterium profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	82.4464	624	1012	95	below_threshold
Microbacterium murale	strain=CCM 7640	GCA_014635185.1	1081040	1081040	type	True	82.0681	656	1012	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	81.3749	571	1012	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.9891	511	1012	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	80.9441	583	1012	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.9259	537	1012	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.7816	407	1012	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.6085	429	1012	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.5281	442	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:32,902] [INFO] DFAST Taxonomy check result was written to GCF_014205075.1_ASM1420507v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:32,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:32,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:32,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference/checkm_data
[2024-01-24 10:47:32,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:32,939] [INFO] Task started: CheckM
[2024-01-24 10:47:32,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205075.1_ASM1420507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205075.1_ASM1420507v1_genomic.fna/checkm_input GCF_014205075.1_ASM1420507v1_genomic.fna/checkm_result
[2024-01-24 10:48:28,244] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:28,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:28,265] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:28,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:28,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205075.1_ASM1420507v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:28,266] [INFO] Task started: Blastn
[2024-01-24 10:48:28,266] [INFO] Running command: blastn -query GCF_014205075.1_ASM1420507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg928c3ac7-1b1a-4c4f-b6a2-7795b830d608/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205075.1_ASM1420507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:30,174] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:30,179] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:30,180] [INFO] Target genome list was writen to GCF_014205075.1_ASM1420507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:30,211] [INFO] Task started: fastANI
[2024-01-24 10:48:30,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a9ea9fc-7516-42f1-bbe2-f798a1514f54/GCF_014205075.1_ASM1420507v1_genomic.fna.gz --refList GCF_014205075.1_ASM1420507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205075.1_ASM1420507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:41,308] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:41,323] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:41,323] [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_014205075.1	s__Microbacterium ginsengiterrae	100.0	1012	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.21	98.43	0.95	0.89	3	conclusive
GCF_007988825.1	s__Microbacterium aerolatum	83.8223	689	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_903645325.1	s__Microbacterium sp903645325	83.6133	630	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277895.1	s__Microbacterium sp015277895	83.6086	697	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635185.1	s__Microbacterium murale	82.0382	659	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105335.1	s__Microbacterium paraoxydans	81.3435	571	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	-
GCF_003610275.1	s__Microbacterium ginsengiterrae_A	81.1907	589	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979475.1	s__Microbacterium sp002979475	81.1189	562	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271365.1	s__Microbacterium sp008271365	81.0391	562	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387575.1	s__Microbacterium sp003387575	80.9141	538	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009758255.1	s__Microbacterium sp009758255	80.8736	533	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268455.1	s__Microbacterium sp018268455	80.4933	418	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552355.1	s__Microbacterium resistens	80.2968	485	1012	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 10:48:41,325] [INFO] GTDB search result was written to GCF_014205075.1_ASM1420507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:41,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:41,329] [INFO] DFAST_QC result json was written to GCF_014205075.1_ASM1420507v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:41,329] [INFO] DFAST_QC completed!
[2024-01-24 10:48:41,329] [INFO] Total running time: 0h1m32s