[2024-01-24 14:22:33,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,389] [INFO] DQC Reference Directory: /var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference
[2024-01-24 14:22:34,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,689] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,689] [INFO] Running command: gunzip -c /var/lib/cwl/stga6867d47-2965-4c27-a7e9-b75a8c6bb711/GCF_000956545.1_ASM95654v1_genomic.fna.gz | prodigal -d GCF_000956545.1_ASM95654v1_genomic.fna/cds.fna -a GCF_000956545.1_ASM95654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,547] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,548] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,548] [INFO] Running command: hmmsearch --tblout GCF_000956545.1_ASM95654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference/reference_markers.hmm GCF_000956545.1_ASM95654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:45,859] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:45,860] [INFO] Found 6/6 markers.
[2024-01-24 14:22:45,901] [INFO] Query marker FASTA was written to GCF_000956545.1_ASM95654v1_genomic.fna/markers.fasta
[2024-01-24 14:22:45,901] [INFO] Task started: Blastn
[2024-01-24 14:22:45,902] [INFO] Running command: blastn -query GCF_000956545.1_ASM95654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference/reference_markers.fasta -out GCF_000956545.1_ASM95654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:47,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:47,357] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:47,357] [INFO] Target genome list was writen to GCF_000956545.1_ASM95654v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:47,367] [INFO] Task started: fastANI
[2024-01-24 14:22:47,367] [INFO] Running command: fastANI --query /var/lib/cwl/stga6867d47-2965-4c27-a7e9-b75a8c6bb711/GCF_000956545.1_ASM95654v1_genomic.fna.gz --refList GCF_000956545.1_ASM95654v1_genomic.fna/target_genomes.txt --output GCF_000956545.1_ASM95654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:00,272] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:00,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:00,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:00,289] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:00,289] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:00,290] [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 azadirachtae	strain=DSM 23848	GCA_000956545.1	582680	582680	type	True	100.0	1305	1308	95	conclusive
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	81.642	613	1308	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	81.5293	543	1308	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.4602	645	1308	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.3295	531	1308	95	below_threshold
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	81.0667	609	1308	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	81.0038	603	1308	95	below_threshold
Microbacterium foliorum	strain=NRRL B-24224	GCA_003367705.1	104336	104336	suspected-type	True	80.5432	599	1308	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	80.5009	596	1308	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	80.3658	595	1308	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	80.2805	436	1308	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	80.2362	443	1308	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	80.1423	505	1308	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.0732	487	1308	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.8378	471	1308	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.7734	500	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:00,291] [INFO] DFAST Taxonomy check result was written to GCF_000956545.1_ASM95654v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:00,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:00,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:00,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference/checkm_data
[2024-01-24 14:23:00,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:00,341] [INFO] Task started: CheckM
[2024-01-24 14:23:00,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000956545.1_ASM95654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000956545.1_ASM95654v1_genomic.fna/checkm_input GCF_000956545.1_ASM95654v1_genomic.fna/checkm_result
[2024-01-24 14:23:56,125] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:56,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:56,185] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:56,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:56,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000956545.1_ASM95654v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:56,186] [INFO] Task started: Blastn
[2024-01-24 14:23:56,186] [INFO] Running command: blastn -query GCF_000956545.1_ASM95654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeac29df9-84c6-477a-b3cb-5862f76ac968/dqc_reference/reference_markers_gtdb.fasta -out GCF_000956545.1_ASM95654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:00,078] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:00,082] [INFO] Selected 10 target genomes.
[2024-01-24 14:24:00,082] [INFO] Target genome list was writen to GCF_000956545.1_ASM95654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:00,091] [INFO] Task started: fastANI
[2024-01-24 14:24:00,091] [INFO] Running command: fastANI --query /var/lib/cwl/stga6867d47-2965-4c27-a7e9-b75a8c6bb711/GCF_000956545.1_ASM95654v1_genomic.fna.gz --refList GCF_000956545.1_ASM95654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000956545.1_ASM95654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:10,748] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:10,762] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:10,762] [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_000956545.1	s__Microbacterium azadirachtae	100.0	1305	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.29	96.06	0.91	0.89	5	conclusive
GCF_902506375.1	s__Microbacterium sp902506375	87.6828	971	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306305.1	s__Microbacterium sp017306305	87.497	955	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.93	98.76	0.92	0.91	3	-
GCA_018268435.1	s__Microbacterium sp018268435	86.8571	672	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257455.1	s__Microbacterium sp002257455	86.5309	854	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956505.1	s__Microbacterium azadirachtae_A	86.1819	980	1308	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.57	96.57	0.89	0.89	2	-
GCA_018268515.1	s__Microbacterium sp018268515	85.9297	792	1308	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	84.9177	725	1308	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	81.4279	648	1308	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	81.3929	688	1308	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 14:24:10,764] [INFO] GTDB search result was written to GCF_000956545.1_ASM95654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:10,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:10,768] [INFO] DFAST_QC result json was written to GCF_000956545.1_ASM95654v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:10,768] [INFO] DFAST_QC completed!
[2024-01-24 14:24:10,768] [INFO] Total running time: 0h1m37s