[2023-06-18 11:02:40,795] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:02:40,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:02:40,798] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference
[2023-06-18 11:02:43,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:02:43,176] [INFO] Task started: Prodigal
[2023-06-18 11:02:43,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a3266a2-6e53-433a-93cf-e901cd640270/GCA_018814205.1_ASM1881420v1_genomic.fna.gz | prodigal -d GCA_018814205.1_ASM1881420v1_genomic.fna/cds.fna -a GCA_018814205.1_ASM1881420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:02:46,059] [INFO] Task succeeded: Prodigal
[2023-06-18 11:02:46,060] [INFO] Task started: HMMsearch
[2023-06-18 11:02:46,060] [INFO] Running command: hmmsearch --tblout GCA_018814205.1_ASM1881420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference/reference_markers.hmm GCA_018814205.1_ASM1881420v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:02:46,230] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:02:46,231] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2a3266a2-6e53-433a-93cf-e901cd640270/GCA_018814205.1_ASM1881420v1_genomic.fna.gz]
[2023-06-18 11:02:46,251] [INFO] Query marker FASTA was written to GCA_018814205.1_ASM1881420v1_genomic.fna/markers.fasta
[2023-06-18 11:02:46,252] [INFO] Task started: Blastn
[2023-06-18 11:02:46,252] [INFO] Running command: blastn -query GCA_018814205.1_ASM1881420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference/reference_markers.fasta -out GCA_018814205.1_ASM1881420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:02:46,763] [INFO] Task succeeded: Blastn
[2023-06-18 11:02:46,766] [INFO] Selected 5 target genomes.
[2023-06-18 11:02:46,766] [INFO] Target genome list was writen to GCA_018814205.1_ASM1881420v1_genomic.fna/target_genomes.txt
[2023-06-18 11:02:46,768] [INFO] Task started: fastANI
[2023-06-18 11:02:46,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a3266a2-6e53-433a-93cf-e901cd640270/GCA_018814205.1_ASM1881420v1_genomic.fna.gz --refList GCA_018814205.1_ASM1881420v1_genomic.fna/target_genomes.txt --output GCA_018814205.1_ASM1881420v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:02:48,446] [INFO] Task succeeded: fastANI
[2023-06-18 11:02:48,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:02:48,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:02:48,449] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:02:48,449] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 11:02:48,449] [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 11:02:48,451] [INFO] DFAST Taxonomy check result was written to GCA_018814205.1_ASM1881420v1_genomic.fna/tc_result.tsv
[2023-06-18 11:02:48,452] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:02:48,452] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:02:48,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference/checkm_data
[2023-06-18 11:02:48,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:02:48,474] [INFO] Task started: CheckM
[2023-06-18 11:02:48,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018814205.1_ASM1881420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018814205.1_ASM1881420v1_genomic.fna/checkm_input GCA_018814205.1_ASM1881420v1_genomic.fna/checkm_result
[2023-06-18 11:03:04,114] [INFO] Task succeeded: CheckM
[2023-06-18 11:03:04,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:03:04,143] [INFO] ===== Completeness check finished =====
[2023-06-18 11:03:04,144] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:03:04,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018814205.1_ASM1881420v1_genomic.fna/markers.fasta)
[2023-06-18 11:03:04,144] [INFO] Task started: Blastn
[2023-06-18 11:03:04,144] [INFO] Running command: blastn -query GCA_018814205.1_ASM1881420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd62336d-f37c-45d4-87cc-aeb66c926eb1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018814205.1_ASM1881420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:03:04,751] [INFO] Task succeeded: Blastn
[2023-06-18 11:03:04,755] [INFO] Selected 9 target genomes.
[2023-06-18 11:03:04,755] [INFO] Target genome list was writen to GCA_018814205.1_ASM1881420v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:03:04,795] [INFO] Task started: fastANI
[2023-06-18 11:03:04,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a3266a2-6e53-433a-93cf-e901cd640270/GCA_018814205.1_ASM1881420v1_genomic.fna.gz --refList GCA_018814205.1_ASM1881420v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018814205.1_ASM1881420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:03:06,758] [INFO] Task succeeded: fastANI
[2023-06-18 11:03:06,761] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:03:06,762] [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_018817005.1	s__JAHIUF01 sp018817005	99.8006	437	475	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__GCA-2686295;g__JAHIUF01	95.0	99.77	99.74	0.93	0.92	3	conclusive
--------------------------------------------------------------------------------
[2023-06-18 11:03:06,766] [INFO] GTDB search result was written to GCA_018814205.1_ASM1881420v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:03:06,769] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:03:06,771] [INFO] DFAST_QC result json was written to GCA_018814205.1_ASM1881420v1_genomic.fna/dqc_result.json
[2023-06-18 11:03:06,772] [INFO] DFAST_QC completed!
[2023-06-18 11:03:06,772] [INFO] Total running time: 0h0m26s