[2023-06-19 09:17:40,221] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:17:40,223] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:17:40,223] [INFO] DQC Reference Directory: /var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference
[2023-06-19 09:17:41,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:17:41,406] [INFO] Task started: Prodigal
[2023-06-19 09:17:41,407] [INFO] Running command: gunzip -c /var/lib/cwl/stg00329968-bba4-433a-bc8d-ad7c56dfe4d2/GCA_018896855.1_ASM1889685v1_genomic.fna.gz | prodigal -d GCA_018896855.1_ASM1889685v1_genomic.fna/cds.fna -a GCA_018896855.1_ASM1889685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:17:45,006] [INFO] Task succeeded: Prodigal
[2023-06-19 09:17:45,006] [INFO] Task started: HMMsearch
[2023-06-19 09:17:45,007] [INFO] Running command: hmmsearch --tblout GCA_018896855.1_ASM1889685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference/reference_markers.hmm GCA_018896855.1_ASM1889685v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:17:45,175] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:17:45,176] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00329968-bba4-433a-bc8d-ad7c56dfe4d2/GCA_018896855.1_ASM1889685v1_genomic.fna.gz]
[2023-06-19 09:17:45,198] [INFO] Query marker FASTA was written to GCA_018896855.1_ASM1889685v1_genomic.fna/markers.fasta
[2023-06-19 09:17:45,198] [INFO] Task started: Blastn
[2023-06-19 09:17:45,198] [INFO] Running command: blastn -query GCA_018896855.1_ASM1889685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference/reference_markers.fasta -out GCA_018896855.1_ASM1889685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:45,760] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:45,763] [INFO] Selected 13 target genomes.
[2023-06-19 09:17:45,764] [INFO] Target genome list was writen to GCA_018896855.1_ASM1889685v1_genomic.fna/target_genomes.txt
[2023-06-19 09:17:45,765] [INFO] Task started: fastANI
[2023-06-19 09:17:45,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg00329968-bba4-433a-bc8d-ad7c56dfe4d2/GCA_018896855.1_ASM1889685v1_genomic.fna.gz --refList GCA_018896855.1_ASM1889685v1_genomic.fna/target_genomes.txt --output GCA_018896855.1_ASM1889685v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:17:51,354] [INFO] Task succeeded: fastANI
[2023-06-19 09:17:51,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:17:51,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:17:51,356] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:17:51,356] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 09:17:51,356] [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 09:17:51,358] [INFO] DFAST Taxonomy check result was written to GCA_018896855.1_ASM1889685v1_genomic.fna/tc_result.tsv
[2023-06-19 09:17:51,359] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:17:51,359] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:17:51,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference/checkm_data
[2023-06-19 09:17:51,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:17:51,386] [INFO] Task started: CheckM
[2023-06-19 09:17:51,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018896855.1_ASM1889685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018896855.1_ASM1889685v1_genomic.fna/checkm_input GCA_018896855.1_ASM1889685v1_genomic.fna/checkm_result
[2023-06-19 09:18:09,184] [INFO] Task succeeded: CheckM
[2023-06-19 09:18:09,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.20%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:18:09,211] [INFO] ===== Completeness check finished =====
[2023-06-19 09:18:09,211] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:18:09,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018896855.1_ASM1889685v1_genomic.fna/markers.fasta)
[2023-06-19 09:18:09,212] [INFO] Task started: Blastn
[2023-06-19 09:18:09,212] [INFO] Running command: blastn -query GCA_018896855.1_ASM1889685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg170d83d8-158b-4187-bc75-fd1079a86b77/dqc_reference/reference_markers_gtdb.fasta -out GCA_018896855.1_ASM1889685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:18:09,983] [INFO] Task succeeded: Blastn
[2023-06-19 09:18:09,986] [INFO] Selected 14 target genomes.
[2023-06-19 09:18:09,986] [INFO] Target genome list was writen to GCA_018896855.1_ASM1889685v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:18:09,987] [INFO] Task started: fastANI
[2023-06-19 09:18:09,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg00329968-bba4-433a-bc8d-ad7c56dfe4d2/GCA_018896855.1_ASM1889685v1_genomic.fna.gz --refList GCA_018896855.1_ASM1889685v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018896855.1_ASM1889685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:18:16,733] [INFO] Task succeeded: fastANI
[2023-06-19 09:18:16,740] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:18:16,740] [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_018812705.1	s__UBA12451 sp018812705	99.4717	479	515	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__Kpj58rc;g__UBA12451	95.0	99.70	99.47	0.95	0.93	3	conclusive
GCA_001805965.1	s__UBA12451 sp001805965	83.9148	382	515	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__Kpj58rc;g__UBA12451	95.0	99.85	99.78	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-19 09:18:16,742] [INFO] GTDB search result was written to GCA_018896855.1_ASM1889685v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:18:16,743] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:18:16,745] [INFO] DFAST_QC result json was written to GCA_018896855.1_ASM1889685v1_genomic.fna/dqc_result.json
[2023-06-19 09:18:16,745] [INFO] DFAST_QC completed!
[2023-06-19 09:18:16,745] [INFO] Total running time: 0h0m37s