[2023-06-18 12:49:14,661] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:49:14,665] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:49:14,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference
[2023-06-18 12:49:16,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:49:16,097] [INFO] Task started: Prodigal
[2023-06-18 12:49:16,097] [INFO] Running command: gunzip -c /var/lib/cwl/stgff355638-497c-4724-8a51-d4ba78d8fd3d/GCA_029554715.1_ASM2955471v1_genomic.fna.gz | prodigal -d GCA_029554715.1_ASM2955471v1_genomic.fna/cds.fna -a GCA_029554715.1_ASM2955471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:49:19,810] [INFO] Task succeeded: Prodigal
[2023-06-18 12:49:19,810] [INFO] Task started: HMMsearch
[2023-06-18 12:49:19,810] [INFO] Running command: hmmsearch --tblout GCA_029554715.1_ASM2955471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference/reference_markers.hmm GCA_029554715.1_ASM2955471v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:49:20,132] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:49:20,135] [INFO] Found 6/6 markers.
[2023-06-18 12:49:20,169] [INFO] Query marker FASTA was written to GCA_029554715.1_ASM2955471v1_genomic.fna/markers.fasta
[2023-06-18 12:49:20,169] [INFO] Task started: Blastn
[2023-06-18 12:49:20,169] [INFO] Running command: blastn -query GCA_029554715.1_ASM2955471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference/reference_markers.fasta -out GCA_029554715.1_ASM2955471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:49:22,737] [INFO] Task succeeded: Blastn
[2023-06-18 12:49:22,743] [INFO] Selected 15 target genomes.
[2023-06-18 12:49:22,744] [INFO] Target genome list was writen to GCA_029554715.1_ASM2955471v1_genomic.fna/target_genomes.txt
[2023-06-18 12:49:22,784] [INFO] Task started: fastANI
[2023-06-18 12:49:22,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgff355638-497c-4724-8a51-d4ba78d8fd3d/GCA_029554715.1_ASM2955471v1_genomic.fna.gz --refList GCA_029554715.1_ASM2955471v1_genomic.fna/target_genomes.txt --output GCA_029554715.1_ASM2955471v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:49:30,015] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:30,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:49:30,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:49:30,017] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 12:49:30,017] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 12:49:30,017] [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 12:49:30,021] [INFO] DFAST Taxonomy check result was written to GCA_029554715.1_ASM2955471v1_genomic.fna/tc_result.tsv
[2023-06-18 12:49:30,022] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:49:30,022] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:49:30,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference/checkm_data
[2023-06-18 12:49:30,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:49:30,052] [INFO] Task started: CheckM
[2023-06-18 12:49:30,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029554715.1_ASM2955471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029554715.1_ASM2955471v1_genomic.fna/checkm_input GCA_029554715.1_ASM2955471v1_genomic.fna/checkm_result
[2023-06-18 12:49:51,254] [INFO] Task succeeded: CheckM
[2023-06-18 12:49:51,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.47%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:49:51,300] [INFO] ===== Completeness check finished =====
[2023-06-18 12:49:51,300] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:49:51,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029554715.1_ASM2955471v1_genomic.fna/markers.fasta)
[2023-06-18 12:49:51,301] [INFO] Task started: Blastn
[2023-06-18 12:49:51,301] [INFO] Running command: blastn -query GCA_029554715.1_ASM2955471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01e7a838-2b03-410d-a11f-baca71bc3e16/dqc_reference/reference_markers_gtdb.fasta -out GCA_029554715.1_ASM2955471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:49:52,324] [INFO] Task succeeded: Blastn
[2023-06-18 12:49:52,328] [INFO] Selected 16 target genomes.
[2023-06-18 12:49:52,329] [INFO] Target genome list was writen to GCA_029554715.1_ASM2955471v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:49:52,345] [INFO] Task started: fastANI
[2023-06-18 12:49:52,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgff355638-497c-4724-8a51-d4ba78d8fd3d/GCA_029554715.1_ASM2955471v1_genomic.fna.gz --refList GCA_029554715.1_ASM2955471v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029554715.1_ASM2955471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:49:58,429] [INFO] Task succeeded: fastANI
[2023-06-18 12:49:58,433] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 12:49:58,434] [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_002418595.1	s__UBA5776 sp002418595	98.2517	267	364	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA5776	95.0	97.72	96.48	0.78	0.69	3	conclusive
GCA_011620275.1	s__UBA5776 sp011620275	92.8187	310	364	d__Bacteria;p__Omnitrophota;c__Koll11;o__GIF10;f__UBA6249;g__UBA5776	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:49:58,437] [INFO] GTDB search result was written to GCA_029554715.1_ASM2955471v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:49:58,439] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:49:58,442] [INFO] DFAST_QC result json was written to GCA_029554715.1_ASM2955471v1_genomic.fna/dqc_result.json
[2023-06-18 12:49:58,442] [INFO] DFAST_QC completed!
[2023-06-18 12:49:58,442] [INFO] Total running time: 0h0m44s