[2023-06-08 03:14:27,020] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:14:27,021] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:14:27,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference
[2023-06-08 03:14:28,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:14:28,281] [INFO] Task started: Prodigal
[2023-06-08 03:14:28,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg19060dbf-f44e-42b5-b2cc-e3ad5b257e86/GCA_945866045.1_MsH-01oct19-327_genomic.fna.gz | prodigal -d GCA_945866045.1_MsH-01oct19-327_genomic.fna/cds.fna -a GCA_945866045.1_MsH-01oct19-327_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:14:37,758] [INFO] Task succeeded: Prodigal
[2023-06-08 03:14:37,758] [INFO] Task started: HMMsearch
[2023-06-08 03:14:37,758] [INFO] Running command: hmmsearch --tblout GCA_945866045.1_MsH-01oct19-327_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference/reference_markers.hmm GCA_945866045.1_MsH-01oct19-327_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:14:38,025] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:14:38,027] [INFO] Found 6/6 markers.
[2023-06-08 03:14:38,060] [INFO] Query marker FASTA was written to GCA_945866045.1_MsH-01oct19-327_genomic.fna/markers.fasta
[2023-06-08 03:14:38,060] [INFO] Task started: Blastn
[2023-06-08 03:14:38,060] [INFO] Running command: blastn -query GCA_945866045.1_MsH-01oct19-327_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference/reference_markers.fasta -out GCA_945866045.1_MsH-01oct19-327_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:14:38,782] [INFO] Task succeeded: Blastn
[2023-06-08 03:14:38,786] [INFO] Selected 27 target genomes.
[2023-06-08 03:14:38,787] [INFO] Target genome list was writen to GCA_945866045.1_MsH-01oct19-327_genomic.fna/target_genomes.txt
[2023-06-08 03:14:38,792] [INFO] Task started: fastANI
[2023-06-08 03:14:38,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg19060dbf-f44e-42b5-b2cc-e3ad5b257e86/GCA_945866045.1_MsH-01oct19-327_genomic.fna.gz --refList GCA_945866045.1_MsH-01oct19-327_genomic.fna/target_genomes.txt --output GCA_945866045.1_MsH-01oct19-327_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:14:57,032] [INFO] Task succeeded: fastANI
[2023-06-08 03:14:57,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:14:57,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:14:57,035] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:14:57,036] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:14:57,036] [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
--------------------------------------------------------------------------------
[2023-06-08 03:14:57,038] [INFO] DFAST Taxonomy check result was written to GCA_945866045.1_MsH-01oct19-327_genomic.fna/tc_result.tsv
[2023-06-08 03:14:57,039] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:14:57,039] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:14:57,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference/checkm_data
[2023-06-08 03:14:57,043] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:14:57,075] [INFO] Task started: CheckM
[2023-06-08 03:14:57,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945866045.1_MsH-01oct19-327_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945866045.1_MsH-01oct19-327_genomic.fna/checkm_input GCA_945866045.1_MsH-01oct19-327_genomic.fna/checkm_result
[2023-06-08 03:15:29,193] [INFO] Task succeeded: CheckM
[2023-06-08 03:15:29,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:15:29,213] [INFO] ===== Completeness check finished =====
[2023-06-08 03:15:29,213] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:15:29,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945866045.1_MsH-01oct19-327_genomic.fna/markers.fasta)
[2023-06-08 03:15:29,214] [INFO] Task started: Blastn
[2023-06-08 03:15:29,214] [INFO] Running command: blastn -query GCA_945866045.1_MsH-01oct19-327_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ef1b6ac-0e87-4834-9d2e-5d7910d39fac/dqc_reference/reference_markers_gtdb.fasta -out GCA_945866045.1_MsH-01oct19-327_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:15:30,398] [INFO] Task succeeded: Blastn
[2023-06-08 03:15:30,402] [INFO] Selected 15 target genomes.
[2023-06-08 03:15:30,402] [INFO] Target genome list was writen to GCA_945866045.1_MsH-01oct19-327_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:15:30,405] [INFO] Task started: fastANI
[2023-06-08 03:15:30,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg19060dbf-f44e-42b5-b2cc-e3ad5b257e86/GCA_945866045.1_MsH-01oct19-327_genomic.fna.gz --refList GCA_945866045.1_MsH-01oct19-327_genomic.fna/target_genomes_gtdb.txt --output GCA_945866045.1_MsH-01oct19-327_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:15:38,878] [INFO] Task succeeded: fastANI
[2023-06-08 03:15:38,892] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:15:38,892] [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
GCA_002737725.1	s__GCA-2737725 sp002737725	99.2875	878	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	99.95	99.95	0.95	0.95	2	conclusive
GCA_009693785.1	s__GCA-2737725 sp009693785	77.453	283	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793085.1	s__GCA-2737725 sp016793085	77.2503	203	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793005.1	s__GCA-2737725 sp016793005	77.1201	207	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297485.1	s__SCTM01 sp004297485	76.7727	66	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SCTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888485.1	s__SHVO01 sp903888485	76.2111	88	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869315.1	s__VGEM01 sp016869315	76.058	91	984	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__VGEM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:15:38,894] [INFO] GTDB search result was written to GCA_945866045.1_MsH-01oct19-327_genomic.fna/result_gtdb.tsv
[2023-06-08 03:15:38,895] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:15:38,898] [INFO] DFAST_QC result json was written to GCA_945866045.1_MsH-01oct19-327_genomic.fna/dqc_result.json
[2023-06-08 03:15:38,898] [INFO] DFAST_QC completed!
[2023-06-08 03:15:38,898] [INFO] Total running time: 0h1m12s