[2023-06-16 22:40:08,095] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:40:08,098] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:40:08,098] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference
[2023-06-16 22:40:09,565] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:40:09,567] [INFO] Task started: Prodigal
[2023-06-16 22:40:09,567] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3d72dd8-6f07-49c1-97d3-03c00e5fc2a4/GCA_013349485.1_ASM1334948v1_genomic.fna.gz | prodigal -d GCA_013349485.1_ASM1334948v1_genomic.fna/cds.fna -a GCA_013349485.1_ASM1334948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:40:17,567] [INFO] Task succeeded: Prodigal
[2023-06-16 22:40:17,568] [INFO] Task started: HMMsearch
[2023-06-16 22:40:17,568] [INFO] Running command: hmmsearch --tblout GCA_013349485.1_ASM1334948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference/reference_markers.hmm GCA_013349485.1_ASM1334948v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:40:17,807] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:40:17,808] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb3d72dd8-6f07-49c1-97d3-03c00e5fc2a4/GCA_013349485.1_ASM1334948v1_genomic.fna.gz]
[2023-06-16 22:40:17,835] [INFO] Query marker FASTA was written to GCA_013349485.1_ASM1334948v1_genomic.fna/markers.fasta
[2023-06-16 22:40:17,835] [INFO] Task started: Blastn
[2023-06-16 22:40:17,835] [INFO] Running command: blastn -query GCA_013349485.1_ASM1334948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference/reference_markers.fasta -out GCA_013349485.1_ASM1334948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:40:18,391] [INFO] Task succeeded: Blastn
[2023-06-16 22:40:18,395] [INFO] Selected 10 target genomes.
[2023-06-16 22:40:18,395] [INFO] Target genome list was writen to GCA_013349485.1_ASM1334948v1_genomic.fna/target_genomes.txt
[2023-06-16 22:40:18,398] [INFO] Task started: fastANI
[2023-06-16 22:40:18,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3d72dd8-6f07-49c1-97d3-03c00e5fc2a4/GCA_013349485.1_ASM1334948v1_genomic.fna.gz --refList GCA_013349485.1_ASM1334948v1_genomic.fna/target_genomes.txt --output GCA_013349485.1_ASM1334948v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:40:28,209] [INFO] Task succeeded: fastANI
[2023-06-16 22:40:28,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:40:28,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:40:28,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:40:28,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:40:28,212] [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 22:40:28,214] [INFO] DFAST Taxonomy check result was written to GCA_013349485.1_ASM1334948v1_genomic.fna/tc_result.tsv
[2023-06-16 22:40:28,215] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:40:28,215] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:40:28,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference/checkm_data
[2023-06-16 22:40:28,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:40:28,257] [INFO] Task started: CheckM
[2023-06-16 22:40:28,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013349485.1_ASM1334948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013349485.1_ASM1334948v1_genomic.fna/checkm_input GCA_013349485.1_ASM1334948v1_genomic.fna/checkm_result
[2023-06-16 22:40:57,264] [INFO] Task succeeded: CheckM
[2023-06-16 22:40:57,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.04%
Contamintation: 3.99%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:40:57,291] [INFO] ===== Completeness check finished =====
[2023-06-16 22:40:57,291] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:40:57,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013349485.1_ASM1334948v1_genomic.fna/markers.fasta)
[2023-06-16 22:40:57,292] [INFO] Task started: Blastn
[2023-06-16 22:40:57,292] [INFO] Running command: blastn -query GCA_013349485.1_ASM1334948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d4d187-77c4-4558-828d-61836312c6e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_013349485.1_ASM1334948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:40:57,801] [INFO] Task succeeded: Blastn
[2023-06-16 22:40:57,805] [INFO] Selected 14 target genomes.
[2023-06-16 22:40:57,806] [INFO] Target genome list was writen to GCA_013349485.1_ASM1334948v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:40:57,823] [INFO] Task started: fastANI
[2023-06-16 22:40:57,823] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3d72dd8-6f07-49c1-97d3-03c00e5fc2a4/GCA_013349485.1_ASM1334948v1_genomic.fna.gz --refList GCA_013349485.1_ASM1334948v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013349485.1_ASM1334948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:41:07,409] [INFO] Task succeeded: fastANI
[2023-06-16 22:41:07,413] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:41:07,414] [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_013349485.1	s__DUZN01 sp013349485	100.0	841	861	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__DUZN01	95.0	98.76	98.76	0.53	0.53	2	conclusive
--------------------------------------------------------------------------------
[2023-06-16 22:41:07,416] [INFO] GTDB search result was written to GCA_013349485.1_ASM1334948v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:41:07,416] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:41:07,418] [INFO] DFAST_QC result json was written to GCA_013349485.1_ASM1334948v1_genomic.fna/dqc_result.json
[2023-06-16 22:41:07,419] [INFO] DFAST_QC completed!
[2023-06-16 22:41:07,419] [INFO] Total running time: 0h0m59s