[2024-01-24 15:01:14,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:14,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:14,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference
[2024-01-24 15:01:15,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:15,882] [INFO] Task started: Prodigal
[2024-01-24 15:01:15,882] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd78fff3-19d8-450f-bbb1-a20c830c72d0/GCF_002741995.1_ASM274199v1_genomic.fna.gz | prodigal -d GCF_002741995.1_ASM274199v1_genomic.fna/cds.fna -a GCF_002741995.1_ASM274199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:23,518] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:23,519] [INFO] Task started: HMMsearch
[2024-01-24 15:01:23,519] [INFO] Running command: hmmsearch --tblout GCF_002741995.1_ASM274199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference/reference_markers.hmm GCF_002741995.1_ASM274199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:23,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:23,770] [INFO] Found 6/6 markers.
[2024-01-24 15:01:23,812] [INFO] Query marker FASTA was written to GCF_002741995.1_ASM274199v1_genomic.fna/markers.fasta
[2024-01-24 15:01:23,813] [INFO] Task started: Blastn
[2024-01-24 15:01:23,813] [INFO] Running command: blastn -query GCF_002741995.1_ASM274199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference/reference_markers.fasta -out GCF_002741995.1_ASM274199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:25,140] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:25,144] [INFO] Selected 14 target genomes.
[2024-01-24 15:01:25,145] [INFO] Target genome list was writen to GCF_002741995.1_ASM274199v1_genomic.fna/target_genomes.txt
[2024-01-24 15:01:25,200] [INFO] Task started: fastANI
[2024-01-24 15:01:25,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd78fff3-19d8-450f-bbb1-a20c830c72d0/GCF_002741995.1_ASM274199v1_genomic.fna.gz --refList GCF_002741995.1_ASM274199v1_genomic.fna/target_genomes.txt --output GCF_002741995.1_ASM274199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:35,568] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:35,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:35,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:35,586] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:01:35,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:35,586] [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 sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	100.0	907	909	95	conclusive
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	100.0	907	909	95	conclusive
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	99.9504	908	909	95	conclusive
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	81.6791	567	909	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	81.4467	520	909	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	81.3905	515	909	95	below_threshold
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	81.3318	531	909	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	80.9693	511	909	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	80.859	451	909	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.2847	470	909	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.1142	434	909	95	below_threshold
Microbacterium pseudoresistens	strain=DSM 22185	GCA_013409745.1	640634	640634	type	True	80.094	419	909	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	80.0688	431	909	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.0387	450	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:35,588] [INFO] DFAST Taxonomy check result was written to GCF_002741995.1_ASM274199v1_genomic.fna/tc_result.tsv
[2024-01-24 15:01:35,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:35,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:35,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference/checkm_data
[2024-01-24 15:01:35,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:35,620] [INFO] Task started: CheckM
[2024-01-24 15:01:35,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002741995.1_ASM274199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002741995.1_ASM274199v1_genomic.fna/checkm_input GCF_002741995.1_ASM274199v1_genomic.fna/checkm_result
[2024-01-24 15:02:16,502] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:16,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:16,523] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:16,523] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:16,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002741995.1_ASM274199v1_genomic.fna/markers.fasta)
[2024-01-24 15:02:16,524] [INFO] Task started: Blastn
[2024-01-24 15:02:16,524] [INFO] Running command: blastn -query GCF_002741995.1_ASM274199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d029bad-7e87-4eeb-ac16-afd477f1b343/dqc_reference/reference_markers_gtdb.fasta -out GCF_002741995.1_ASM274199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:18,890] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:18,894] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:18,894] [INFO] Target genome list was writen to GCF_002741995.1_ASM274199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:18,909] [INFO] Task started: fastANI
[2024-01-24 15:02:18,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd78fff3-19d8-450f-bbb1-a20c830c72d0/GCF_002741995.1_ASM274199v1_genomic.fna.gz --refList GCF_002741995.1_ASM274199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002741995.1_ASM274199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:28,472] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:28,487] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:28,487] [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_004564075.1	s__Microbacterium sediminis	99.9504	908	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	conclusive
GCF_015235415.1	s__Microbacterium paludicola_A	82.4542	559	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001426925.1	s__Microbacterium sp001426925	82.428	547	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_016805985.1	s__Microbacterium sp016805985	82.0919	568	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735645.1	s__Microbacterium oryzae	81.469	519	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592545.1	s__Microbacterium sp017592545	81.3069	534	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422385.1	s__Microbacterium indicum	81.2377	495	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970975.1	s__Microbacterium halophytorum	80.9566	512	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	80.868	450	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_902506375.1	s__Microbacterium sp902506375	80.1679	468	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409745.1	s__Microbacterium pseudoresistens	80.1171	417	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898315.1	s__Microbacterium sp001898315	80.1105	450	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_016907355.1	s__Agromyces aurantiacus	79.0184	426	909	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:28,489] [INFO] GTDB search result was written to GCF_002741995.1_ASM274199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:28,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:28,494] [INFO] DFAST_QC result json was written to GCF_002741995.1_ASM274199v1_genomic.fna/dqc_result.json
[2024-01-24 15:02:28,494] [INFO] DFAST_QC completed!
[2024-01-24 15:02:28,494] [INFO] Total running time: 0h1m14s