[2023-06-28 17:56:56,199] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:56:56,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:56:56,208] [INFO] DQC Reference Directory: /var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference
[2023-06-28 17:56:57,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:56:57,612] [INFO] Task started: Prodigal
[2023-06-28 17:56:57,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d711633-fd7a-41c1-9dc2-293a798390cf/GCA_017467585.1_ASM1746758v1_genomic.fna.gz | prodigal -d GCA_017467585.1_ASM1746758v1_genomic.fna/cds.fna -a GCA_017467585.1_ASM1746758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:57:00,180] [INFO] Task succeeded: Prodigal
[2023-06-28 17:57:00,180] [INFO] Task started: HMMsearch
[2023-06-28 17:57:00,180] [INFO] Running command: hmmsearch --tblout GCA_017467585.1_ASM1746758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference/reference_markers.hmm GCA_017467585.1_ASM1746758v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:57:00,443] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:57:00,445] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d711633-fd7a-41c1-9dc2-293a798390cf/GCA_017467585.1_ASM1746758v1_genomic.fna.gz]
[2023-06-28 17:57:00,464] [INFO] Query marker FASTA was written to GCA_017467585.1_ASM1746758v1_genomic.fna/markers.fasta
[2023-06-28 17:57:00,464] [INFO] Task started: Blastn
[2023-06-28 17:57:00,464] [INFO] Running command: blastn -query GCA_017467585.1_ASM1746758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference/reference_markers.fasta -out GCA_017467585.1_ASM1746758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:57:01,047] [INFO] Task succeeded: Blastn
[2023-06-28 17:57:01,053] [INFO] Selected 15 target genomes.
[2023-06-28 17:57:01,054] [INFO] Target genome list was writen to GCA_017467585.1_ASM1746758v1_genomic.fna/target_genomes.txt
[2023-06-28 17:57:01,057] [INFO] Task started: fastANI
[2023-06-28 17:57:01,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d711633-fd7a-41c1-9dc2-293a798390cf/GCA_017467585.1_ASM1746758v1_genomic.fna.gz --refList GCA_017467585.1_ASM1746758v1_genomic.fna/target_genomes.txt --output GCA_017467585.1_ASM1746758v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:57:05,913] [INFO] Task succeeded: fastANI
[2023-06-28 17:57:05,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:57:05,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:57:05,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:57:05,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:57:05,917] [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
--------------------------------------------------------------------------------
[2023-06-28 17:57:05,919] [INFO] DFAST Taxonomy check result was written to GCA_017467585.1_ASM1746758v1_genomic.fna/tc_result.tsv
[2023-06-28 17:57:05,920] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:57:05,920] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:57:05,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference/checkm_data
[2023-06-28 17:57:05,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:57:05,935] [INFO] Task started: CheckM
[2023-06-28 17:57:05,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017467585.1_ASM1746758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017467585.1_ASM1746758v1_genomic.fna/checkm_input GCA_017467585.1_ASM1746758v1_genomic.fna/checkm_result
[2023-06-28 17:57:22,021] [INFO] Task succeeded: CheckM
[2023-06-28 17:57:22,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:57:22,043] [INFO] ===== Completeness check finished =====
[2023-06-28 17:57:22,043] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:57:22,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017467585.1_ASM1746758v1_genomic.fna/markers.fasta)
[2023-06-28 17:57:22,044] [INFO] Task started: Blastn
[2023-06-28 17:57:22,044] [INFO] Running command: blastn -query GCA_017467585.1_ASM1746758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb643a123-cd09-4884-9f4e-484128ee7ab2/dqc_reference/reference_markers_gtdb.fasta -out GCA_017467585.1_ASM1746758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:57:22,821] [INFO] Task succeeded: Blastn
[2023-06-28 17:57:22,826] [INFO] Selected 22 target genomes.
[2023-06-28 17:57:22,826] [INFO] Target genome list was writen to GCA_017467585.1_ASM1746758v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:57:22,848] [INFO] Task started: fastANI
[2023-06-28 17:57:22,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d711633-fd7a-41c1-9dc2-293a798390cf/GCA_017467585.1_ASM1746758v1_genomic.fna.gz --refList GCA_017467585.1_ASM1746758v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017467585.1_ASM1746758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:57:27,292] [INFO] Task succeeded: fastANI
[2023-06-28 17:57:27,295] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:57:27,295] [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_017467585.1	s__RGIG4790 sp017467585	100.0	322	323	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__RGIG4790	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-28 17:57:27,297] [INFO] GTDB search result was written to GCA_017467585.1_ASM1746758v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:57:27,298] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:57:27,301] [INFO] DFAST_QC result json was written to GCA_017467585.1_ASM1746758v1_genomic.fna/dqc_result.json
[2023-06-28 17:57:27,302] [INFO] DFAST_QC completed!
[2023-06-28 17:57:27,302] [INFO] Total running time: 0h0m31s