[2023-06-29 19:34:08,871] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:34:08,873] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:34:08,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference
[2023-06-29 19:34:10,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:34:10,664] [INFO] Task started: Prodigal
[2023-06-29 19:34:10,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ac079eb-a597-45a8-861b-c80d28831eb5/GCA_021841925.1_ASM2184192v1_genomic.fna.gz | prodigal -d GCA_021841925.1_ASM2184192v1_genomic.fna/cds.fna -a GCA_021841925.1_ASM2184192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:34:17,499] [INFO] Task succeeded: Prodigal
[2023-06-29 19:34:17,499] [INFO] Task started: HMMsearch
[2023-06-29 19:34:17,499] [INFO] Running command: hmmsearch --tblout GCA_021841925.1_ASM2184192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference/reference_markers.hmm GCA_021841925.1_ASM2184192v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:34:17,745] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:34:17,747] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8ac079eb-a597-45a8-861b-c80d28831eb5/GCA_021841925.1_ASM2184192v1_genomic.fna.gz]
[2023-06-29 19:34:17,786] [INFO] Query marker FASTA was written to GCA_021841925.1_ASM2184192v1_genomic.fna/markers.fasta
[2023-06-29 19:34:17,787] [INFO] Task started: Blastn
[2023-06-29 19:34:17,787] [INFO] Running command: blastn -query GCA_021841925.1_ASM2184192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference/reference_markers.fasta -out GCA_021841925.1_ASM2184192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:34:19,466] [INFO] Task succeeded: Blastn
[2023-06-29 19:34:19,471] [INFO] Selected 5 target genomes.
[2023-06-29 19:34:19,472] [INFO] Target genome list was writen to GCA_021841925.1_ASM2184192v1_genomic.fna/target_genomes.txt
[2023-06-29 19:34:19,474] [INFO] Task started: fastANI
[2023-06-29 19:34:19,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ac079eb-a597-45a8-861b-c80d28831eb5/GCA_021841925.1_ASM2184192v1_genomic.fna.gz --refList GCA_021841925.1_ASM2184192v1_genomic.fna/target_genomes.txt --output GCA_021841925.1_ASM2184192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:34:22,867] [INFO] Task succeeded: fastANI
[2023-06-29 19:34:22,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:34:22,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:34:22,870] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:34:22,870] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:34:22,871] [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
--------------------------------------------------------------------------------
[2023-06-29 19:34:22,873] [INFO] DFAST Taxonomy check result was written to GCA_021841925.1_ASM2184192v1_genomic.fna/tc_result.tsv
[2023-06-29 19:34:22,874] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:34:22,874] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:34:22,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference/checkm_data
[2023-06-29 19:34:22,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:34:22,918] [INFO] Task started: CheckM
[2023-06-29 19:34:22,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021841925.1_ASM2184192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021841925.1_ASM2184192v1_genomic.fna/checkm_input GCA_021841925.1_ASM2184192v1_genomic.fna/checkm_result
[2023-06-29 19:34:49,604] [INFO] Task succeeded: CheckM
[2023-06-29 19:34:49,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.11%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 19:34:49,633] [INFO] ===== Completeness check finished =====
[2023-06-29 19:34:49,634] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:34:49,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021841925.1_ASM2184192v1_genomic.fna/markers.fasta)
[2023-06-29 19:34:49,634] [INFO] Task started: Blastn
[2023-06-29 19:34:49,635] [INFO] Running command: blastn -query GCA_021841925.1_ASM2184192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e495d5d-0cc2-4c06-b44d-074051bff348/dqc_reference/reference_markers_gtdb.fasta -out GCA_021841925.1_ASM2184192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:34:50,304] [INFO] Task succeeded: Blastn
[2023-06-29 19:34:50,308] [INFO] Selected 9 target genomes.
[2023-06-29 19:34:50,308] [INFO] Target genome list was writen to GCA_021841925.1_ASM2184192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:34:50,314] [INFO] Task started: fastANI
[2023-06-29 19:34:50,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ac079eb-a597-45a8-861b-c80d28831eb5/GCA_021841925.1_ASM2184192v1_genomic.fna.gz --refList GCA_021841925.1_ASM2184192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021841925.1_ASM2184192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:34:55,858] [INFO] Task succeeded: fastANI
[2023-06-29 19:34:55,864] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:34:55,864] [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_013044165.1	s__JABEVB01 sp013044165	85.3926	108	459	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__WQYP01;f__WQYP01;g__JABEVB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044065.1	s__JABEVA01 sp013044065	82.8494	73	459	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__WQYP01;f__WQYP01;g__JABEVA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:34:55,866] [INFO] GTDB search result was written to GCA_021841925.1_ASM2184192v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:34:55,867] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:34:55,869] [INFO] DFAST_QC result json was written to GCA_021841925.1_ASM2184192v1_genomic.fna/dqc_result.json
[2023-06-29 19:34:55,870] [INFO] DFAST_QC completed!
[2023-06-29 19:34:55,870] [INFO] Total running time: 0h0m47s