[2024-01-24 15:09:55,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,444] [INFO] DQC Reference Directory: /var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference
[2024-01-24 15:09:58,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,167] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dd0c87d-2f78-47dd-91f9-831331ed187a/GCF_900445095.1_48290_F02_genomic.fna.gz | prodigal -d GCF_900445095.1_48290_F02_genomic.fna/cds.fna -a GCF_900445095.1_48290_F02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:03,383] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:03,384] [INFO] Task started: HMMsearch
[2024-01-24 15:10:03,384] [INFO] Running command: hmmsearch --tblout GCF_900445095.1_48290_F02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference/reference_markers.hmm GCF_900445095.1_48290_F02_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:03,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:03,669] [INFO] Found 6/6 markers.
[2024-01-24 15:10:03,705] [INFO] Query marker FASTA was written to GCF_900445095.1_48290_F02_genomic.fna/markers.fasta
[2024-01-24 15:10:03,706] [INFO] Task started: Blastn
[2024-01-24 15:10:03,706] [INFO] Running command: blastn -query GCF_900445095.1_48290_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference/reference_markers.fasta -out GCF_900445095.1_48290_F02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:04,396] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:04,401] [INFO] Selected 8 target genomes.
[2024-01-24 15:10:04,401] [INFO] Target genome list was writen to GCF_900445095.1_48290_F02_genomic.fna/target_genomes.txt
[2024-01-24 15:10:04,438] [INFO] Task started: fastANI
[2024-01-24 15:10:04,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dd0c87d-2f78-47dd-91f9-831331ed187a/GCF_900445095.1_48290_F02_genomic.fna.gz --refList GCF_900445095.1_48290_F02_genomic.fna/target_genomes.txt --output GCF_900445095.1_48290_F02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:09,749] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:09,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:09,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:09,757] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:10:09,757] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:09,758] [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
Aerococcus viridans	strain=NCTC8251	GCA_900445095.1	1377	1377	suspected-type	True	100.0	749	753	95	conclusive
Aerococcus viridans	strain=CCUG4311	GCA_001543285.1	1377	1377	suspected-type	True	99.9934	729	753	95	conclusive
Aerococcus viridans	strain=ATCC 11563	GCA_000178435.1	1377	1377	suspected-type	True	99.8551	594	753	95	conclusive
Aerococcus urinaeequi	strain=CCUG28094	GCA_001543205.1	51665	51665	type	True	93.9813	557	753	95	below_threshold
Aerococcus urinaeequi	strain=DSM 20341	GCA_000425085.1	51665	51665	suspected-type	True	93.8194	552	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:09,761] [INFO] DFAST Taxonomy check result was written to GCF_900445095.1_48290_F02_genomic.fna/tc_result.tsv
[2024-01-24 15:10:09,761] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:09,762] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:09,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference/checkm_data
[2024-01-24 15:10:09,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:09,802] [INFO] Task started: CheckM
[2024-01-24 15:10:09,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445095.1_48290_F02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445095.1_48290_F02_genomic.fna/checkm_input GCF_900445095.1_48290_F02_genomic.fna/checkm_result
[2024-01-24 15:10:35,037] [INFO] Task succeeded: CheckM
[2024-01-24 15:10:35,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 15:10:35,062] [INFO] ===== Completeness check finished =====
[2024-01-24 15:10:35,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:10:35,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445095.1_48290_F02_genomic.fna/markers.fasta)
[2024-01-24 15:10:35,063] [INFO] Task started: Blastn
[2024-01-24 15:10:35,063] [INFO] Running command: blastn -query GCF_900445095.1_48290_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stgb425c46f-03db-4ee4-b522-48ead3c7bbc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445095.1_48290_F02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:35,866] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:35,871] [INFO] Selected 6 target genomes.
[2024-01-24 15:10:35,871] [INFO] Target genome list was writen to GCF_900445095.1_48290_F02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:10:35,878] [INFO] Task started: fastANI
[2024-01-24 15:10:35,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dd0c87d-2f78-47dd-91f9-831331ed187a/GCF_900445095.1_48290_F02_genomic.fna.gz --refList GCF_900445095.1_48290_F02_genomic.fna/target_genomes_gtdb.txt --output GCF_900445095.1_48290_F02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:10:39,776] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:39,782] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:10:39,782] [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_001543285.1	s__Aerococcus viridans	99.9934	729	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	99.21	97.63	0.94	0.82	4	conclusive
GCF_002083135.2	s__Aerococcus viridans_C	94.6008	566	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440555.1	s__Aerococcus sp002440555	94.1556	511	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001543205.1	s__Aerococcus urinaeequi	93.9915	558	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	96.56	95.91	0.88	0.83	18	-
GCF_002871935.1	s__Aerococcus viridans_B	84.5451	456	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	98.96	98.96	0.91	0.91	2	-
GCF_003797145.1	s__Aerococcus sp003797145	80.837	294	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Aerococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:10:39,784] [INFO] GTDB search result was written to GCF_900445095.1_48290_F02_genomic.fna/result_gtdb.tsv
[2024-01-24 15:10:39,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:10:39,790] [INFO] DFAST_QC result json was written to GCF_900445095.1_48290_F02_genomic.fna/dqc_result.json
[2024-01-24 15:10:39,790] [INFO] DFAST_QC completed!
[2024-01-24 15:10:39,791] [INFO] Total running time: 0h0m44s