[2023-06-18 10:35:44,471] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:35:44,473] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:35:44,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference
[2023-06-18 10:35:45,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:35:45,756] [INFO] Task started: Prodigal
[2023-06-18 10:35:45,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c1b079f-dc2b-4c9d-9ac3-0f2844acb434/GCA_018239815.1_ASM1823981v1_genomic.fna.gz | prodigal -d GCA_018239815.1_ASM1823981v1_genomic.fna/cds.fna -a GCA_018239815.1_ASM1823981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:35:49,024] [INFO] Task succeeded: Prodigal
[2023-06-18 10:35:49,024] [INFO] Task started: HMMsearch
[2023-06-18 10:35:49,025] [INFO] Running command: hmmsearch --tblout GCA_018239815.1_ASM1823981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference/reference_markers.hmm GCA_018239815.1_ASM1823981v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:35:49,280] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:35:49,283] [INFO] Found 6/6 markers.
[2023-06-18 10:35:49,312] [INFO] Query marker FASTA was written to GCA_018239815.1_ASM1823981v1_genomic.fna/markers.fasta
[2023-06-18 10:35:49,313] [INFO] Task started: Blastn
[2023-06-18 10:35:49,313] [INFO] Running command: blastn -query GCA_018239815.1_ASM1823981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference/reference_markers.fasta -out GCA_018239815.1_ASM1823981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:35:49,942] [INFO] Task succeeded: Blastn
[2023-06-18 10:35:49,955] [INFO] Selected 14 target genomes.
[2023-06-18 10:35:49,956] [INFO] Target genome list was writen to GCA_018239815.1_ASM1823981v1_genomic.fna/target_genomes.txt
[2023-06-18 10:35:49,963] [INFO] Task started: fastANI
[2023-06-18 10:35:49,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c1b079f-dc2b-4c9d-9ac3-0f2844acb434/GCA_018239815.1_ASM1823981v1_genomic.fna.gz --refList GCA_018239815.1_ASM1823981v1_genomic.fna/target_genomes.txt --output GCA_018239815.1_ASM1823981v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:35:57,518] [INFO] Task succeeded: fastANI
[2023-06-18 10:35:57,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:35:57,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:35:57,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 10:35:57,526] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 10:35:57,526] [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 10:35:57,528] [INFO] DFAST Taxonomy check result was written to GCA_018239815.1_ASM1823981v1_genomic.fna/tc_result.tsv
[2023-06-18 10:35:57,529] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:35:57,529] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:35:57,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference/checkm_data
[2023-06-18 10:35:57,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:35:57,552] [INFO] Task started: CheckM
[2023-06-18 10:35:57,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018239815.1_ASM1823981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018239815.1_ASM1823981v1_genomic.fna/checkm_input GCA_018239815.1_ASM1823981v1_genomic.fna/checkm_result
[2023-06-18 10:36:15,918] [INFO] Task succeeded: CheckM
[2023-06-18 10:36:15,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:36:15,951] [INFO] ===== Completeness check finished =====
[2023-06-18 10:36:15,951] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:36:15,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018239815.1_ASM1823981v1_genomic.fna/markers.fasta)
[2023-06-18 10:36:15,952] [INFO] Task started: Blastn
[2023-06-18 10:36:15,952] [INFO] Running command: blastn -query GCA_018239815.1_ASM1823981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b21299-4425-4fbe-9b94-e74356310c5e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018239815.1_ASM1823981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:36:16,726] [INFO] Task succeeded: Blastn
[2023-06-18 10:36:16,730] [INFO] Selected 17 target genomes.
[2023-06-18 10:36:16,731] [INFO] Target genome list was writen to GCA_018239815.1_ASM1823981v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:36:16,787] [INFO] Task started: fastANI
[2023-06-18 10:36:16,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c1b079f-dc2b-4c9d-9ac3-0f2844acb434/GCA_018239815.1_ASM1823981v1_genomic.fna.gz --refList GCA_018239815.1_ASM1823981v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018239815.1_ASM1823981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:36:24,489] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:24,496] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:36:24,496] [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_018239815.1	s__SZAS-3 sp018239815	100.0	494	497	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__JAAKFR01;g__SZAS-3	95.0	99.95	99.95	0.98	0.98	2	conclusive
--------------------------------------------------------------------------------
[2023-06-18 10:36:24,501] [INFO] GTDB search result was written to GCA_018239815.1_ASM1823981v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:36:24,502] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:36:24,507] [INFO] DFAST_QC result json was written to GCA_018239815.1_ASM1823981v1_genomic.fna/dqc_result.json
[2023-06-18 10:36:24,507] [INFO] DFAST_QC completed!
[2023-06-18 10:36:24,507] [INFO] Total running time: 0h0m40s