[2023-07-01 03:19:52,615] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:19:52,639] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:19:52,639] [INFO] DQC Reference Directory: /var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference
[2023-07-01 03:19:53,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:19:53,996] [INFO] Task started: Prodigal
[2023-07-01 03:19:53,997] [INFO] Running command: gunzip -c /var/lib/cwl/stg53ff4716-d0a8-46cb-8fde-8d6758e092f0/GCA_016192575.1_ASM1619257v1_genomic.fna.gz | prodigal -d GCA_016192575.1_ASM1619257v1_genomic.fna/cds.fna -a GCA_016192575.1_ASM1619257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:19:56,991] [INFO] Task succeeded: Prodigal
[2023-07-01 03:19:56,992] [INFO] Task started: HMMsearch
[2023-07-01 03:19:56,992] [INFO] Running command: hmmsearch --tblout GCA_016192575.1_ASM1619257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference/reference_markers.hmm GCA_016192575.1_ASM1619257v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:19:57,231] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:19:57,232] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg53ff4716-d0a8-46cb-8fde-8d6758e092f0/GCA_016192575.1_ASM1619257v1_genomic.fna.gz]
[2023-07-01 03:19:57,257] [INFO] Query marker FASTA was written to GCA_016192575.1_ASM1619257v1_genomic.fna/markers.fasta
[2023-07-01 03:19:57,257] [INFO] Task started: Blastn
[2023-07-01 03:19:57,257] [INFO] Running command: blastn -query GCA_016192575.1_ASM1619257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference/reference_markers.fasta -out GCA_016192575.1_ASM1619257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:19:57,917] [INFO] Task succeeded: Blastn
[2023-07-01 03:19:57,920] [INFO] Selected 22 target genomes.
[2023-07-01 03:19:57,921] [INFO] Target genome list was writen to GCA_016192575.1_ASM1619257v1_genomic.fna/target_genomes.txt
[2023-07-01 03:19:57,926] [INFO] Task started: fastANI
[2023-07-01 03:19:57,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ff4716-d0a8-46cb-8fde-8d6758e092f0/GCA_016192575.1_ASM1619257v1_genomic.fna.gz --refList GCA_016192575.1_ASM1619257v1_genomic.fna/target_genomes.txt --output GCA_016192575.1_ASM1619257v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:20:15,971] [INFO] Task succeeded: fastANI
[2023-07-01 03:20:15,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:20:15,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:20:15,973] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:20:15,973] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 03:20:15,974] [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
--------------------------------------------------------------------------------
[2023-07-01 03:20:15,976] [INFO] DFAST Taxonomy check result was written to GCA_016192575.1_ASM1619257v1_genomic.fna/tc_result.tsv
[2023-07-01 03:20:15,976] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:20:15,976] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:20:15,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference/checkm_data
[2023-07-01 03:20:15,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:20:16,007] [INFO] Task started: CheckM
[2023-07-01 03:20:16,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016192575.1_ASM1619257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016192575.1_ASM1619257v1_genomic.fna/checkm_input GCA_016192575.1_ASM1619257v1_genomic.fna/checkm_result
[2023-07-01 03:20:33,450] [INFO] Task succeeded: CheckM
[2023-07-01 03:20:33,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.04%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 03:20:33,475] [INFO] ===== Completeness check finished =====
[2023-07-01 03:20:33,476] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:20:33,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016192575.1_ASM1619257v1_genomic.fna/markers.fasta)
[2023-07-01 03:20:33,477] [INFO] Task started: Blastn
[2023-07-01 03:20:33,477] [INFO] Running command: blastn -query GCA_016192575.1_ASM1619257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce284063-ef06-4a20-b770-7373580545d2/dqc_reference/reference_markers_gtdb.fasta -out GCA_016192575.1_ASM1619257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:20:34,413] [INFO] Task succeeded: Blastn
[2023-07-01 03:20:34,418] [INFO] Selected 17 target genomes.
[2023-07-01 03:20:34,418] [INFO] Target genome list was writen to GCA_016192575.1_ASM1619257v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:20:34,455] [INFO] Task started: fastANI
[2023-07-01 03:20:34,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg53ff4716-d0a8-46cb-8fde-8d6758e092f0/GCA_016192575.1_ASM1619257v1_genomic.fna.gz --refList GCA_016192575.1_ASM1619257v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016192575.1_ASM1619257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:20:43,651] [INFO] Task succeeded: fastANI
[2023-07-01 03:20:43,660] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 03:20:43,660] [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_016180705.1	s__JACPAU01 sp016180705	83.7435	138	219	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__JACPAU01;g__JACPAU01	95.0	96.92	96.92	0.61	0.61	2	-
GCA_001771285.1	s__2-02-FULL-66-22 sp001771285	76.6741	51	219	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Methylomirabilales;f__2-02-FULL-66-22;g__2-02-FULL-66-22	95.0	99.46	99.46	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-07-01 03:20:43,662] [INFO] GTDB search result was written to GCA_016192575.1_ASM1619257v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:20:43,663] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:20:43,666] [INFO] DFAST_QC result json was written to GCA_016192575.1_ASM1619257v1_genomic.fna/dqc_result.json
[2023-07-01 03:20:43,666] [INFO] DFAST_QC completed!
[2023-07-01 03:20:43,667] [INFO] Total running time: 0h0m51s