[2023-06-16 20:58:29,383] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:58:29,385] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:58:29,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference
[2023-06-16 20:58:30,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:58:30,667] [INFO] Task started: Prodigal
[2023-06-16 20:58:30,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg4de4171f-07f9-4327-9dc9-1227f091572e/GCA_028692765.1_ASM2869276v1_genomic.fna.gz | prodigal -d GCA_028692765.1_ASM2869276v1_genomic.fna/cds.fna -a GCA_028692765.1_ASM2869276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:58:33,652] [INFO] Task succeeded: Prodigal
[2023-06-16 20:58:33,653] [INFO] Task started: HMMsearch
[2023-06-16 20:58:33,653] [INFO] Running command: hmmsearch --tblout GCA_028692765.1_ASM2869276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference/reference_markers.hmm GCA_028692765.1_ASM2869276v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:58:33,831] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:58:33,832] [INFO] Found 6/6 markers.
[2023-06-16 20:58:33,845] [INFO] Query marker FASTA was written to GCA_028692765.1_ASM2869276v1_genomic.fna/markers.fasta
[2023-06-16 20:58:33,845] [INFO] Task started: Blastn
[2023-06-16 20:58:33,845] [INFO] Running command: blastn -query GCA_028692765.1_ASM2869276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference/reference_markers.fasta -out GCA_028692765.1_ASM2869276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:58:34,427] [INFO] Task succeeded: Blastn
[2023-06-16 20:58:34,430] [INFO] Selected 15 target genomes.
[2023-06-16 20:58:34,431] [INFO] Target genome list was writen to GCA_028692765.1_ASM2869276v1_genomic.fna/target_genomes.txt
[2023-06-16 20:58:34,436] [INFO] Task started: fastANI
[2023-06-16 20:58:34,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg4de4171f-07f9-4327-9dc9-1227f091572e/GCA_028692765.1_ASM2869276v1_genomic.fna.gz --refList GCA_028692765.1_ASM2869276v1_genomic.fna/target_genomes.txt --output GCA_028692765.1_ASM2869276v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:58:43,026] [INFO] Task succeeded: fastANI
[2023-06-16 20:58:43,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:58:43,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:58:43,029] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:58:43,029] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 20:58:43,029] [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
--------------------------------------------------------------------------------
[2023-06-16 20:58:43,032] [INFO] DFAST Taxonomy check result was written to GCA_028692765.1_ASM2869276v1_genomic.fna/tc_result.tsv
[2023-06-16 20:58:43,032] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:58:43,032] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:58:43,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference/checkm_data
[2023-06-16 20:58:43,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:58:43,047] [INFO] Task started: CheckM
[2023-06-16 20:58:43,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028692765.1_ASM2869276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028692765.1_ASM2869276v1_genomic.fna/checkm_input GCA_028692765.1_ASM2869276v1_genomic.fna/checkm_result
[2023-06-16 20:58:58,100] [INFO] Task succeeded: CheckM
[2023-06-16 20:58:58,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:58:58,154] [INFO] ===== Completeness check finished =====
[2023-06-16 20:58:58,154] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:58:58,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028692765.1_ASM2869276v1_genomic.fna/markers.fasta)
[2023-06-16 20:58:58,156] [INFO] Task started: Blastn
[2023-06-16 20:58:58,156] [INFO] Running command: blastn -query GCA_028692765.1_ASM2869276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cabd4ad-7816-4d54-9be7-7e9bae9db0ee/dqc_reference/reference_markers_gtdb.fasta -out GCA_028692765.1_ASM2869276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:58:58,918] [INFO] Task succeeded: Blastn
[2023-06-16 20:58:58,922] [INFO] Selected 20 target genomes.
[2023-06-16 20:58:58,922] [INFO] Target genome list was writen to GCA_028692765.1_ASM2869276v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:58:58,935] [INFO] Task started: fastANI
[2023-06-16 20:58:58,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg4de4171f-07f9-4327-9dc9-1227f091572e/GCA_028692765.1_ASM2869276v1_genomic.fna.gz --refList GCA_028692765.1_ASM2869276v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028692765.1_ASM2869276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:59:04,004] [INFO] Task succeeded: fastANI
[2023-06-16 20:59:04,008] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 20:59:04,009] [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_002070735.1	s__GCA-002841655 sp002070735	82.6703	179	281	d__Bacteria;p__Patescibacteria;c__ABY1;o__BM507;f__UBA12465;g__GCA-002841655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903937325.1	s__GCA-002841655 sp903937325	78.0861	75	281	d__Bacteria;p__Patescibacteria;c__ABY1;o__BM507;f__UBA12465;g__GCA-002841655	95.0	99.71	99.71	0.92	0.92	2	-
GCA_016938835.1	s__GCA-002841655 sp016938835	77.7675	57	281	d__Bacteria;p__Patescibacteria;c__ABY1;o__BM507;f__UBA12465;g__GCA-002841655	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:59:04,010] [INFO] GTDB search result was written to GCA_028692765.1_ASM2869276v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:59:04,011] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:59:04,013] [INFO] DFAST_QC result json was written to GCA_028692765.1_ASM2869276v1_genomic.fna/dqc_result.json
[2023-06-16 20:59:04,014] [INFO] DFAST_QC completed!
[2023-06-16 20:59:04,014] [INFO] Total running time: 0h0m35s