[2023-06-19 13:54:07,915] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:07,917] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:07,917] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference
[2023-06-19 13:54:10,067] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:10,069] [INFO] Task started: Prodigal
[2023-06-19 13:54:10,069] [INFO] Running command: gunzip -c /var/lib/cwl/stgb744bc71-2614-456f-a7e1-30a1db9432ec/GCA_018433625.1_SV1_genomic.fna.gz | prodigal -d GCA_018433625.1_SV1_genomic.fna/cds.fna -a GCA_018433625.1_SV1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:17,549] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:17,550] [INFO] Task started: HMMsearch
[2023-06-19 13:54:17,550] [INFO] Running command: hmmsearch --tblout GCA_018433625.1_SV1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference/reference_markers.hmm GCA_018433625.1_SV1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:17,818] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:17,819] [INFO] Found 6/6 markers.
[2023-06-19 13:54:17,849] [INFO] Query marker FASTA was written to GCA_018433625.1_SV1_genomic.fna/markers.fasta
[2023-06-19 13:54:17,850] [INFO] Task started: Blastn
[2023-06-19 13:54:17,850] [INFO] Running command: blastn -query GCA_018433625.1_SV1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference/reference_markers.fasta -out GCA_018433625.1_SV1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:18,493] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:18,497] [INFO] Selected 16 target genomes.
[2023-06-19 13:54:18,498] [INFO] Target genome list was writen to GCA_018433625.1_SV1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:18,504] [INFO] Task started: fastANI
[2023-06-19 13:54:18,504] [INFO] Running command: fastANI --query /var/lib/cwl/stgb744bc71-2614-456f-a7e1-30a1db9432ec/GCA_018433625.1_SV1_genomic.fna.gz --refList GCA_018433625.1_SV1_genomic.fna/target_genomes.txt --output GCA_018433625.1_SV1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:29,683] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:29,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:29,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:29,686] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:54:29,687] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:54:29,687] [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
--------------------------------------------------------------------------------
[2023-06-19 13:54:29,690] [INFO] DFAST Taxonomy check result was written to GCA_018433625.1_SV1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:29,690] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:29,691] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:29,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference/checkm_data
[2023-06-19 13:54:29,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:29,729] [INFO] Task started: CheckM
[2023-06-19 13:54:29,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018433625.1_SV1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018433625.1_SV1_genomic.fna/checkm_input GCA_018433625.1_SV1_genomic.fna/checkm_result
[2023-06-19 13:54:56,845] [INFO] Task succeeded: CheckM
[2023-06-19 13:54:56,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:54:56,867] [INFO] ===== Completeness check finished =====
[2023-06-19 13:54:56,867] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:54:56,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018433625.1_SV1_genomic.fna/markers.fasta)
[2023-06-19 13:54:56,868] [INFO] Task started: Blastn
[2023-06-19 13:54:56,868] [INFO] Running command: blastn -query GCA_018433625.1_SV1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a29a2d9-b6f5-4e78-bc0c-7ec1dd24175d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018433625.1_SV1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:57,729] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:57,734] [INFO] Selected 16 target genomes.
[2023-06-19 13:54:57,735] [INFO] Target genome list was writen to GCA_018433625.1_SV1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:54:57,792] [INFO] Task started: fastANI
[2023-06-19 13:54:57,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgb744bc71-2614-456f-a7e1-30a1db9432ec/GCA_018433625.1_SV1_genomic.fna.gz --refList GCA_018433625.1_SV1_genomic.fna/target_genomes_gtdb.txt --output GCA_018433625.1_SV1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:55:05,126] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:05,135] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:55:05,135] [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_001603165.1	s__UBA2256 sp001603165	99.3614	652	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA2256	95.0	99.40	98.46	0.90	0.81	14	conclusive
GCA_002383375.1	s__UBA2256 sp002383375	81.6182	511	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA2256	95.0	99.59	99.59	0.92	0.92	2	-
GCA_002428725.1	s__UBA2256 sp002428725	80.3392	487	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA2256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839205.1	s__UBA11090 sp002839205	77.5761	99	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA11090	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016926955.1	s__JAFGNN01 sp016926955	77.4084	51	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008080685.1	s__VKGY01 sp008080685	77.2592	137	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__VKGY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262985.1	s__JAFGNN01 sp018262985	76.8445	60	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	98.32	98.32	0.96	0.96	2	-
GCA_012517645.1	s__JAAYUR01 sp012517645	76.5665	62	930	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAAYUR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:55:05,137] [INFO] GTDB search result was written to GCA_018433625.1_SV1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:55:05,138] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:55:05,142] [INFO] DFAST_QC result json was written to GCA_018433625.1_SV1_genomic.fna/dqc_result.json
[2023-06-19 13:55:05,142] [INFO] DFAST_QC completed!
[2023-06-19 13:55:05,142] [INFO] Total running time: 0h0m57s