[2024-01-25 17:41:05,689] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:05,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:05,692] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference
[2024-01-25 17:41:06,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:06,917] [INFO] Task started: Prodigal
[2024-01-25 17:41:06,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg665987d2-1bd1-4d70-91ce-d23868e58da0/GCF_025234735.1_ASM2523473v1_genomic.fna.gz | prodigal -d GCF_025234735.1_ASM2523473v1_genomic.fna/cds.fna -a GCF_025234735.1_ASM2523473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:13,257] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:13,257] [INFO] Task started: HMMsearch
[2024-01-25 17:41:13,257] [INFO] Running command: hmmsearch --tblout GCF_025234735.1_ASM2523473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference/reference_markers.hmm GCF_025234735.1_ASM2523473v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:13,512] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:13,513] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg665987d2-1bd1-4d70-91ce-d23868e58da0/GCF_025234735.1_ASM2523473v1_genomic.fna.gz]
[2024-01-25 17:41:13,542] [INFO] Query marker FASTA was written to GCF_025234735.1_ASM2523473v1_genomic.fna/markers.fasta
[2024-01-25 17:41:13,542] [INFO] Task started: Blastn
[2024-01-25 17:41:13,542] [INFO] Running command: blastn -query GCF_025234735.1_ASM2523473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference/reference_markers.fasta -out GCF_025234735.1_ASM2523473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:14,098] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:14,102] [INFO] Selected 7 target genomes.
[2024-01-25 17:41:14,102] [INFO] Target genome list was writen to GCF_025234735.1_ASM2523473v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:14,122] [INFO] Task started: fastANI
[2024-01-25 17:41:14,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg665987d2-1bd1-4d70-91ce-d23868e58da0/GCF_025234735.1_ASM2523473v1_genomic.fna.gz --refList GCF_025234735.1_ASM2523473v1_genomic.fna/target_genomes.txt --output GCF_025234735.1_ASM2523473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:41:18,709] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:18,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:41:18,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:41:18,716] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:41:18,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:41:18,716] [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
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	100.0	844	851	95	conclusive
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	87.5972	695	851	95	below_threshold
Exiguobacterium marinum	strain=DSM 16307	GCA_000620845.1	273528	273528	type	True	87.5526	722	851	95	below_threshold
Exiguobacterium qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	86.0885	683	851	95	below_threshold
Exiguobacterium algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	83.2108	536	851	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	81.0865	452	851	95	below_threshold
Exiguobacterium alkaliphilum	strain=12/1	GCA_000714435.1	1428684	1428684	type	True	81.0092	477	851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:41:18,718] [INFO] DFAST Taxonomy check result was written to GCF_025234735.1_ASM2523473v1_genomic.fna/tc_result.tsv
[2024-01-25 17:41:18,718] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:41:18,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:41:18,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference/checkm_data
[2024-01-25 17:41:18,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:41:18,748] [INFO] Task started: CheckM
[2024-01-25 17:41:18,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025234735.1_ASM2523473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025234735.1_ASM2523473v1_genomic.fna/checkm_input GCF_025234735.1_ASM2523473v1_genomic.fna/checkm_result
[2024-01-25 17:41:42,781] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:42,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:42,801] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:42,801] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:42,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025234735.1_ASM2523473v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:42,802] [INFO] Task started: Blastn
[2024-01-25 17:41:42,802] [INFO] Running command: blastn -query GCF_025234735.1_ASM2523473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb605f9f-a1b4-4c4d-9ddb-d6ea2d405f88/dqc_reference/reference_markers_gtdb.fasta -out GCF_025234735.1_ASM2523473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:43,625] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:43,628] [INFO] Selected 7 target genomes.
[2024-01-25 17:41:43,628] [INFO] Target genome list was writen to GCF_025234735.1_ASM2523473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:43,641] [INFO] Task started: fastANI
[2024-01-25 17:41:43,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg665987d2-1bd1-4d70-91ce-d23868e58da0/GCF_025234735.1_ASM2523473v1_genomic.fna.gz --refList GCF_025234735.1_ASM2523473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025234735.1_ASM2523473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:48,503] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:48,509] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:48,509] [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_018617485.1	s__Exiguobacterium sp018617485	100.0	850	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.75	95.34	0.91	0.90	6	conclusive
GCF_001908175.1	s__Exiguobacterium sp001908175	90.5536	729	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.57	95.32	0.91	0.90	6	-
GCF_001909285.1	s__Exiguobacterium profundum_A	87.5815	737	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.55	95.32	0.92	0.88	29	-
GCF_000620845.1	s__Exiguobacterium marinum	87.5526	722	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.37	97.95	0.94	0.94	10	-
GCF_018617395.1	s__Exiguobacterium sp018617395	87.5511	735	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	97.92	96.72	0.94	0.91	3	-
GCA_902362975.1	s__Exiguobacterium sp902362975	87.1206	665	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.52	95.12	0.85	0.82	3	-
GCF_018617855.1	s__Exiguobacterium sp018617855	86.0885	683	851	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:48,511] [INFO] GTDB search result was written to GCF_025234735.1_ASM2523473v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:48,511] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:48,514] [INFO] DFAST_QC result json was written to GCF_025234735.1_ASM2523473v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:48,514] [INFO] DFAST_QC completed!
[2024-01-25 17:41:48,514] [INFO] Total running time: 0h0m43s