[2024-01-24 12:06:14,118] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,120] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference
[2024-01-24 12:06:15,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,528] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,529] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5484409-7001-4659-96a0-31d4d70ee817/GCF_017592545.1_ASM1759254v1_genomic.fna.gz | prodigal -d GCF_017592545.1_ASM1759254v1_genomic.fna/cds.fna -a GCF_017592545.1_ASM1759254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,739] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,740] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,740] [INFO] Running command: hmmsearch --tblout GCF_017592545.1_ASM1759254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference/reference_markers.hmm GCF_017592545.1_ASM1759254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:26,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:26,035] [INFO] Found 6/6 markers.
[2024-01-24 12:06:26,068] [INFO] Query marker FASTA was written to GCF_017592545.1_ASM1759254v1_genomic.fna/markers.fasta
[2024-01-24 12:06:26,069] [INFO] Task started: Blastn
[2024-01-24 12:06:26,069] [INFO] Running command: blastn -query GCF_017592545.1_ASM1759254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference/reference_markers.fasta -out GCF_017592545.1_ASM1759254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:27,528] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:27,531] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:27,532] [INFO] Target genome list was writen to GCF_017592545.1_ASM1759254v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:27,537] [INFO] Task started: fastANI
[2024-01-24 12:06:27,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5484409-7001-4659-96a0-31d4d70ee817/GCF_017592545.1_ASM1759254v1_genomic.fna.gz --refList GCF_017592545.1_ASM1759254v1_genomic.fna/target_genomes.txt --output GCF_017592545.1_ASM1759254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:37,362] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:37,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:37,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:37,373] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:37,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:37,373] [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 stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	100.0	1140	1187	95	conclusive
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	82.2468	651	1187	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	81.4037	536	1187	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	81.3399	531	1187	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	81.2985	537	1187	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.8947	500	1187	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.027	488	1187	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.962	440	1187	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.9247	471	1187	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.7506	444	1187	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.6861	486	1187	95	below_threshold
Microbacterium luticocti	strain=DSM 19459	GCA_000422405.1	451764	451764	type	True	79.2278	421	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,382] [INFO] DFAST Taxonomy check result was written to GCF_017592545.1_ASM1759254v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:37,383] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:37,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:37,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference/checkm_data
[2024-01-24 12:06:37,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:37,452] [INFO] Task started: CheckM
[2024-01-24 12:06:37,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017592545.1_ASM1759254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017592545.1_ASM1759254v1_genomic.fna/checkm_input GCF_017592545.1_ASM1759254v1_genomic.fna/checkm_result
[2024-01-24 12:07:32,084] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:32,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:32,110] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:32,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:32,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017592545.1_ASM1759254v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:32,111] [INFO] Task started: Blastn
[2024-01-24 12:07:32,111] [INFO] Running command: blastn -query GCF_017592545.1_ASM1759254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0912e074-4dd2-4214-a088-f52f50b06ab2/dqc_reference/reference_markers_gtdb.fasta -out GCF_017592545.1_ASM1759254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:34,299] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:34,303] [INFO] Selected 5 target genomes.
[2024-01-24 12:07:34,303] [INFO] Target genome list was writen to GCF_017592545.1_ASM1759254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:34,308] [INFO] Task started: fastANI
[2024-01-24 12:07:34,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5484409-7001-4659-96a0-31d4d70ee817/GCF_017592545.1_ASM1759254v1_genomic.fna.gz --refList GCF_017592545.1_ASM1759254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017592545.1_ASM1759254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:39,251] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:39,260] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:39,261] [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_017592545.1	s__Microbacterium sp017592545	100.0	1146	1187	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_015235415.1	s__Microbacterium paludicola_A	83.6119	698	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016805985.1	s__Microbacterium sp016805985	83.3217	721	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426925.1	s__Microbacterium sp001426925	83.0304	643	1187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_014643695.1	s__Microbacterium album	81.3139	536	1187	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 12:07:39,262] [INFO] GTDB search result was written to GCF_017592545.1_ASM1759254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:39,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:39,266] [INFO] DFAST_QC result json was written to GCF_017592545.1_ASM1759254v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:39,266] [INFO] DFAST_QC completed!
[2024-01-24 12:07:39,266] [INFO] Total running time: 0h1m25s