[2023-06-18 14:24:27,582] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:24:27,585] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:24:27,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference
[2023-06-18 14:24:29,016] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:24:29,017] [INFO] Task started: Prodigal
[2023-06-18 14:24:29,017] [INFO] Running command: gunzip -c /var/lib/cwl/stg25252a42-0e07-4b36-99f6-8f322beca03d/GCA_018659445.1_ASM1865944v1_genomic.fna.gz | prodigal -d GCA_018659445.1_ASM1865944v1_genomic.fna/cds.fna -a GCA_018659445.1_ASM1865944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:24:30,565] [INFO] Task succeeded: Prodigal
[2023-06-18 14:24:30,565] [INFO] Task started: HMMsearch
[2023-06-18 14:24:30,566] [INFO] Running command: hmmsearch --tblout GCA_018659445.1_ASM1865944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference/reference_markers.hmm GCA_018659445.1_ASM1865944v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:24:30,829] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:24:30,832] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg25252a42-0e07-4b36-99f6-8f322beca03d/GCA_018659445.1_ASM1865944v1_genomic.fna.gz]
[2023-06-18 14:24:30,859] [INFO] Query marker FASTA was written to GCA_018659445.1_ASM1865944v1_genomic.fna/markers.fasta
[2023-06-18 14:24:30,859] [INFO] Task started: Blastn
[2023-06-18 14:24:30,860] [INFO] Running command: blastn -query GCA_018659445.1_ASM1865944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference/reference_markers.fasta -out GCA_018659445.1_ASM1865944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:24:32,982] [INFO] Task succeeded: Blastn
[2023-06-18 14:24:32,987] [INFO] Selected 5 target genomes.
[2023-06-18 14:24:32,987] [INFO] Target genome list was writen to GCA_018659445.1_ASM1865944v1_genomic.fna/target_genomes.txt
[2023-06-18 14:24:32,992] [INFO] Task started: fastANI
[2023-06-18 14:24:32,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg25252a42-0e07-4b36-99f6-8f322beca03d/GCA_018659445.1_ASM1865944v1_genomic.fna.gz --refList GCA_018659445.1_ASM1865944v1_genomic.fna/target_genomes.txt --output GCA_018659445.1_ASM1865944v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:24:34,582] [INFO] Task succeeded: fastANI
[2023-06-18 14:24:34,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:24:34,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:24:34,585] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:24:34,585] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 14:24:34,585] [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
--------------------------------------------------------------------------------
[2023-06-18 14:24:34,589] [INFO] DFAST Taxonomy check result was written to GCA_018659445.1_ASM1865944v1_genomic.fna/tc_result.tsv
[2023-06-18 14:24:34,589] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:24:34,590] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:24:34,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference/checkm_data
[2023-06-18 14:24:34,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:24:34,613] [INFO] Task started: CheckM
[2023-06-18 14:24:34,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018659445.1_ASM1865944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018659445.1_ASM1865944v1_genomic.fna/checkm_input GCA_018659445.1_ASM1865944v1_genomic.fna/checkm_result
[2023-06-18 14:24:50,225] [INFO] Task succeeded: CheckM
[2023-06-18 14:24:50,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 14:24:50,251] [INFO] ===== Completeness check finished =====
[2023-06-18 14:24:50,251] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:24:50,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018659445.1_ASM1865944v1_genomic.fna/markers.fasta)
[2023-06-18 14:24:50,252] [INFO] Task started: Blastn
[2023-06-18 14:24:50,252] [INFO] Running command: blastn -query GCA_018659445.1_ASM1865944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28dc601c-9f14-45f4-832d-a553d76711cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_018659445.1_ASM1865944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:24:50,835] [INFO] Task succeeded: Blastn
[2023-06-18 14:24:50,840] [INFO] Selected 8 target genomes.
[2023-06-18 14:24:50,840] [INFO] Target genome list was writen to GCA_018659445.1_ASM1865944v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:24:50,846] [INFO] Task started: fastANI
[2023-06-18 14:24:50,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg25252a42-0e07-4b36-99f6-8f322beca03d/GCA_018659445.1_ASM1865944v1_genomic.fna.gz --refList GCA_018659445.1_ASM1865944v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018659445.1_ASM1865944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:24:52,162] [INFO] Task succeeded: fastANI
[2023-06-18 14:24:52,166] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 14:24:52,166] [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_018692925.1	s__BS150m-G60 sp018692925	99.7665	282	308	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR17;g__BS150m-G60	95.0	99.90	99.76	0.95	0.92	8	conclusive
GCA_016784245.1	s__BS150m-G60 sp016784245	87.9343	109	308	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR17;g__BS150m-G60	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 14:24:52,168] [INFO] GTDB search result was written to GCA_018659445.1_ASM1865944v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:24:52,168] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:24:52,171] [INFO] DFAST_QC result json was written to GCA_018659445.1_ASM1865944v1_genomic.fna/dqc_result.json
[2023-06-18 14:24:52,171] [INFO] DFAST_QC completed!
[2023-06-18 14:24:52,171] [INFO] Total running time: 0h0m25s