[2023-06-27 11:39:13,726] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:39:13,751] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:39:13,751] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference
[2023-06-27 11:39:15,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:39:15,536] [INFO] Task started: Prodigal
[2023-06-27 11:39:15,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d2e112b-08ca-4dca-8b09-19b3c0c86f84/GCA_027406705.1_ASM2740670v1_genomic.fna.gz | prodigal -d GCA_027406705.1_ASM2740670v1_genomic.fna/cds.fna -a GCA_027406705.1_ASM2740670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:39:18,835] [INFO] Task succeeded: Prodigal
[2023-06-27 11:39:18,835] [INFO] Task started: HMMsearch
[2023-06-27 11:39:18,835] [INFO] Running command: hmmsearch --tblout GCA_027406705.1_ASM2740670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference/reference_markers.hmm GCA_027406705.1_ASM2740670v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:39:19,044] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:39:19,045] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7d2e112b-08ca-4dca-8b09-19b3c0c86f84/GCA_027406705.1_ASM2740670v1_genomic.fna.gz]
[2023-06-27 11:39:19,070] [INFO] Query marker FASTA was written to GCA_027406705.1_ASM2740670v1_genomic.fna/markers.fasta
[2023-06-27 11:39:19,070] [INFO] Task started: Blastn
[2023-06-27 11:39:19,070] [INFO] Running command: blastn -query GCA_027406705.1_ASM2740670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference/reference_markers.fasta -out GCA_027406705.1_ASM2740670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:39:19,578] [INFO] Task succeeded: Blastn
[2023-06-27 11:39:19,582] [INFO] Selected 15 target genomes.
[2023-06-27 11:39:19,582] [INFO] Target genome list was writen to GCA_027406705.1_ASM2740670v1_genomic.fna/target_genomes.txt
[2023-06-27 11:39:19,584] [INFO] Task started: fastANI
[2023-06-27 11:39:19,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2e112b-08ca-4dca-8b09-19b3c0c86f84/GCA_027406705.1_ASM2740670v1_genomic.fna.gz --refList GCA_027406705.1_ASM2740670v1_genomic.fna/target_genomes.txt --output GCA_027406705.1_ASM2740670v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:39:33,493] [INFO] Task succeeded: fastANI
[2023-06-27 11:39:33,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:39:33,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:39:33,495] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:39:33,495] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:39:33,495] [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
--------------------------------------------------------------------------------
[2023-06-27 11:39:33,497] [INFO] DFAST Taxonomy check result was written to GCA_027406705.1_ASM2740670v1_genomic.fna/tc_result.tsv
[2023-06-27 11:39:33,497] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:39:33,498] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:39:33,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference/checkm_data
[2023-06-27 11:39:33,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:39:33,520] [INFO] Task started: CheckM
[2023-06-27 11:39:33,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027406705.1_ASM2740670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027406705.1_ASM2740670v1_genomic.fna/checkm_input GCA_027406705.1_ASM2740670v1_genomic.fna/checkm_result
[2023-06-27 11:39:49,295] [INFO] Task succeeded: CheckM
[2023-06-27 11:39:49,297] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 6.20%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:39:49,317] [INFO] ===== Completeness check finished =====
[2023-06-27 11:39:49,317] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:39:49,317] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027406705.1_ASM2740670v1_genomic.fna/markers.fasta)
[2023-06-27 11:39:49,317] [INFO] Task started: Blastn
[2023-06-27 11:39:49,317] [INFO] Running command: blastn -query GCA_027406705.1_ASM2740670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbfcaf1a-3667-498a-924c-8afb95789003/dqc_reference/reference_markers_gtdb.fasta -out GCA_027406705.1_ASM2740670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:39:49,814] [INFO] Task succeeded: Blastn
[2023-06-27 11:39:49,817] [INFO] Selected 15 target genomes.
[2023-06-27 11:39:49,817] [INFO] Target genome list was writen to GCA_027406705.1_ASM2740670v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:39:49,822] [INFO] Task started: fastANI
[2023-06-27 11:39:49,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2e112b-08ca-4dca-8b09-19b3c0c86f84/GCA_027406705.1_ASM2740670v1_genomic.fna.gz --refList GCA_027406705.1_ASM2740670v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027406705.1_ASM2740670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:39:56,625] [INFO] Task succeeded: fastANI
[2023-06-27 11:39:56,629] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:39:56,629] [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_013036105.1	s__Rubrimentiphilum sp013036105	76.9676	57	329	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Rubrimentiphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151115.1	s__Rubrimentiphilum sp003151115	76.7738	65	329	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Rubrimentiphilum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003155175.1	s__Hemerobacter limicola	76.6188	55	329	d__Bacteria;p__Eremiobacterota;c__Eremiobacteria;o__Baltobacterales;f__Baltobacteraceae;g__Hemerobacter	95.0	99.36	99.32	0.90	0.89	6	-
--------------------------------------------------------------------------------
[2023-06-27 11:39:56,630] [INFO] GTDB search result was written to GCA_027406705.1_ASM2740670v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:39:56,631] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:39:56,633] [INFO] DFAST_QC result json was written to GCA_027406705.1_ASM2740670v1_genomic.fna/dqc_result.json
[2023-06-27 11:39:56,633] [INFO] DFAST_QC completed!
[2023-06-27 11:39:56,633] [INFO] Total running time: 0h0m43s