[2023-06-17 11:44:30,417] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:44:30,418] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:44:30,419] [INFO] DQC Reference Directory: /var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference
[2023-06-17 11:44:31,741] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:44:31,742] [INFO] Task started: Prodigal
[2023-06-17 11:44:31,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ee33f6b-8d63-4b86-bd32-f5fbd24bb86c/GCA_028284385.1_ASM2828438v1_genomic.fna.gz | prodigal -d GCA_028284385.1_ASM2828438v1_genomic.fna/cds.fna -a GCA_028284385.1_ASM2828438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:44:58,186] [INFO] Task succeeded: Prodigal
[2023-06-17 11:44:58,187] [INFO] Task started: HMMsearch
[2023-06-17 11:44:58,187] [INFO] Running command: hmmsearch --tblout GCA_028284385.1_ASM2828438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference/reference_markers.hmm GCA_028284385.1_ASM2828438v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:44:58,495] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:44:58,497] [INFO] Found 6/6 markers.
[2023-06-17 11:44:58,545] [INFO] Query marker FASTA was written to GCA_028284385.1_ASM2828438v1_genomic.fna/markers.fasta
[2023-06-17 11:44:58,546] [INFO] Task started: Blastn
[2023-06-17 11:44:58,546] [INFO] Running command: blastn -query GCA_028284385.1_ASM2828438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference/reference_markers.fasta -out GCA_028284385.1_ASM2828438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:44:59,189] [INFO] Task succeeded: Blastn
[2023-06-17 11:44:59,198] [INFO] Selected 12 target genomes.
[2023-06-17 11:44:59,198] [INFO] Target genome list was writen to GCA_028284385.1_ASM2828438v1_genomic.fna/target_genomes.txt
[2023-06-17 11:44:59,203] [INFO] Task started: fastANI
[2023-06-17 11:44:59,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee33f6b-8d63-4b86-bd32-f5fbd24bb86c/GCA_028284385.1_ASM2828438v1_genomic.fna.gz --refList GCA_028284385.1_ASM2828438v1_genomic.fna/target_genomes.txt --output GCA_028284385.1_ASM2828438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:45:07,718] [INFO] Task succeeded: fastANI
[2023-06-17 11:45:07,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:45:07,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:45:07,723] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:45:07,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:45:07,723] [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
Pelagicoccus enzymogenes	strain=NFK12	GCA_014803405.1	2773457	2773457	type	True	76.0242	66	1759	95	below_threshold
Pelagicoccus mobilis	strain=KCTC 13126	GCA_016595505.1	415221	415221	type	True	75.7917	62	1759	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:45:07,726] [INFO] DFAST Taxonomy check result was written to GCA_028284385.1_ASM2828438v1_genomic.fna/tc_result.tsv
[2023-06-17 11:45:07,727] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:45:07,727] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:45:07,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference/checkm_data
[2023-06-17 11:45:07,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:45:07,786] [INFO] Task started: CheckM
[2023-06-17 11:45:07,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028284385.1_ASM2828438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028284385.1_ASM2828438v1_genomic.fna/checkm_input GCA_028284385.1_ASM2828438v1_genomic.fna/checkm_result
[2023-06-17 11:46:20,397] [INFO] Task succeeded: CheckM
[2023-06-17 11:46:20,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:46:20,425] [INFO] ===== Completeness check finished =====
[2023-06-17 11:46:20,425] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:46:20,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028284385.1_ASM2828438v1_genomic.fna/markers.fasta)
[2023-06-17 11:46:20,426] [INFO] Task started: Blastn
[2023-06-17 11:46:20,426] [INFO] Running command: blastn -query GCA_028284385.1_ASM2828438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga474a6c6-7061-4124-a632-41f1beebe5b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_028284385.1_ASM2828438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:46:21,410] [INFO] Task succeeded: Blastn
[2023-06-17 11:46:21,416] [INFO] Selected 25 target genomes.
[2023-06-17 11:46:21,416] [INFO] Target genome list was writen to GCA_028284385.1_ASM2828438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:46:21,472] [INFO] Task started: fastANI
[2023-06-17 11:46:21,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee33f6b-8d63-4b86-bd32-f5fbd24bb86c/GCA_028284385.1_ASM2828438v1_genomic.fna.gz --refList GCA_028284385.1_ASM2828438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028284385.1_ASM2828438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:46:36,183] [INFO] Task succeeded: fastANI
[2023-06-17 11:46:36,192] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 11:46:36,192] [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_000155695.1	s__Pelagicoccus sp000155695	76.1821	51	1759	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014803405.1	s__Pelagicoccus sp014803405	76.0242	66	1759	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595505.1	s__Pelagicoccus mobilis	75.7917	62	1759	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Pelagicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:46:36,194] [INFO] GTDB search result was written to GCA_028284385.1_ASM2828438v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:46:36,195] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:46:36,198] [INFO] DFAST_QC result json was written to GCA_028284385.1_ASM2828438v1_genomic.fna/dqc_result.json
[2023-06-17 11:46:36,198] [INFO] DFAST_QC completed!
[2023-06-17 11:46:36,198] [INFO] Total running time: 0h2m6s