[2024-01-24 13:25:31,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:31,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:31,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference
[2024-01-24 13:25:33,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:33,040] [INFO] Task started: Prodigal
[2024-01-24 13:25:33,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e954c48-cdc8-4be2-8b6d-409dfd6dd801/GCF_000416965.1_23.K55_genomic.fna.gz | prodigal -d GCF_000416965.1_23.K55_genomic.fna/cds.fna -a GCF_000416965.1_23.K55_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,070] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,070] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,070] [INFO] Running command: hmmsearch --tblout GCF_000416965.1_23.K55_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference/reference_markers.hmm GCF_000416965.1_23.K55_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:42,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:42,360] [INFO] Found 6/6 markers.
[2024-01-24 13:25:42,391] [INFO] Query marker FASTA was written to GCF_000416965.1_23.K55_genomic.fna/markers.fasta
[2024-01-24 13:25:42,392] [INFO] Task started: Blastn
[2024-01-24 13:25:42,392] [INFO] Running command: blastn -query GCF_000416965.1_23.K55_genomic.fna/markers.fasta -db /var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference/reference_markers.fasta -out GCF_000416965.1_23.K55_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:42,995] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:42,998] [INFO] Selected 12 target genomes.
[2024-01-24 13:25:42,998] [INFO] Target genome list was writen to GCF_000416965.1_23.K55_genomic.fna/target_genomes.txt
[2024-01-24 13:25:43,004] [INFO] Task started: fastANI
[2024-01-24 13:25:43,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e954c48-cdc8-4be2-8b6d-409dfd6dd801/GCF_000416965.1_23.K55_genomic.fna.gz --refList GCF_000416965.1_23.K55_genomic.fna/target_genomes.txt --output GCF_000416965.1_23.K55_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:50,856] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:50,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:50,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:50,866] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:50,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:50,866] [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 chiriqhucha	strain=RW-2	GCA_000416965.1	1385984	1385984	type	True	100.0	995	997	95	conclusive
Exiguobacterium alkaliphilum	strain=12/1	GCA_000714435.1	1428684	1428684	type	True	84.5074	753	997	95	below_threshold
Exiguobacterium aurantiacum	strain=DSM 6208	GCA_000702585.1	33987	33987	type	True	84.4813	773	997	95	below_threshold
Exiguobacterium aurantiacum	strain=NCTC13163	GCA_900450545.1	33987	33987	type	True	84.4251	778	997	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	83.6883	687	997	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	81.2324	529	997	95	below_threshold
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	81.0861	530	997	95	below_threshold
Exiguobacterium algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	81.0301	508	997	95	below_threshold
Exiguobacterium qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	81.0215	515	997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:50,872] [INFO] DFAST Taxonomy check result was written to GCF_000416965.1_23.K55_genomic.fna/tc_result.tsv
[2024-01-24 13:25:50,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:50,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:50,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference/checkm_data
[2024-01-24 13:25:50,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:50,910] [INFO] Task started: CheckM
[2024-01-24 13:25:50,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000416965.1_23.K55_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000416965.1_23.K55_genomic.fna/checkm_input GCF_000416965.1_23.K55_genomic.fna/checkm_result
[2024-01-24 13:26:22,135] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:22,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:22,158] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:22,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:22,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000416965.1_23.K55_genomic.fna/markers.fasta)
[2024-01-24 13:26:22,159] [INFO] Task started: Blastn
[2024-01-24 13:26:22,159] [INFO] Running command: blastn -query GCF_000416965.1_23.K55_genomic.fna/markers.fasta -db /var/lib/cwl/stg107c03a3-6d30-4afa-9dce-30baf8edd60d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000416965.1_23.K55_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:22,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:22,947] [INFO] Selected 7 target genomes.
[2024-01-24 13:26:22,948] [INFO] Target genome list was writen to GCF_000416965.1_23.K55_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:22,955] [INFO] Task started: fastANI
[2024-01-24 13:26:22,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e954c48-cdc8-4be2-8b6d-409dfd6dd801/GCF_000416965.1_23.K55_genomic.fna.gz --refList GCF_000416965.1_23.K55_genomic.fna/target_genomes_gtdb.txt --output GCF_000416965.1_23.K55_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:27,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:27,916] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:27,916] [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_000416965.1	s__Exiguobacterium chiriqhucha	100.0	995	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.87	95.58	0.92	0.89	18	conclusive
GCF_018616375.1	s__Exiguobacterium sp018616375	93.9185	889	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018618415.1	s__Exiguobacterium sp018618415	92.6698	866	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005960665.1	s__Exiguobacterium mexicanum	91.2666	794	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	97.16	96.68	0.89	0.87	17	-
GCF_003467445.1	s__Exiguobacterium sp003467445	91.2281	818	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003331145.1	s__Exiguobacterium sp003331145	90.1766	814	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336985.1	s__Exiguobacterium sp004336985	89.8615	859	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.45	98.45	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:27,917] [INFO] GTDB search result was written to GCF_000416965.1_23.K55_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:27,918] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:27,921] [INFO] DFAST_QC result json was written to GCF_000416965.1_23.K55_genomic.fna/dqc_result.json
[2024-01-24 13:26:27,921] [INFO] DFAST_QC completed!
[2024-01-24 13:26:27,921] [INFO] Total running time: 0h0m56s