[2023-06-29 13:38:41,625] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:38:41,628] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:38:41,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference
[2023-06-29 13:38:42,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:38:42,864] [INFO] Task started: Prodigal
[2023-06-29 13:38:42,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bf24a84-0819-48a6-b6c4-05839a047424/GCA_932190865.1_0308_S_metabat.018_genomic.fna.gz | prodigal -d GCA_932190865.1_0308_S_metabat.018_genomic.fna/cds.fna -a GCA_932190865.1_0308_S_metabat.018_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:38:44,776] [INFO] Task succeeded: Prodigal
[2023-06-29 13:38:44,776] [INFO] Task started: HMMsearch
[2023-06-29 13:38:44,776] [INFO] Running command: hmmsearch --tblout GCA_932190865.1_0308_S_metabat.018_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference/reference_markers.hmm GCA_932190865.1_0308_S_metabat.018_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:38:44,988] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:38:44,990] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bf24a84-0819-48a6-b6c4-05839a047424/GCA_932190865.1_0308_S_metabat.018_genomic.fna.gz]
[2023-06-29 13:38:45,010] [INFO] Query marker FASTA was written to GCA_932190865.1_0308_S_metabat.018_genomic.fna/markers.fasta
[2023-06-29 13:38:45,010] [INFO] Task started: Blastn
[2023-06-29 13:38:45,010] [INFO] Running command: blastn -query GCA_932190865.1_0308_S_metabat.018_genomic.fna/markers.fasta -db /var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference/reference_markers.fasta -out GCA_932190865.1_0308_S_metabat.018_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:38:45,582] [INFO] Task succeeded: Blastn
[2023-06-29 13:38:45,587] [INFO] Selected 13 target genomes.
[2023-06-29 13:38:45,587] [INFO] Target genome list was writen to GCA_932190865.1_0308_S_metabat.018_genomic.fna/target_genomes.txt
[2023-06-29 13:38:45,592] [INFO] Task started: fastANI
[2023-06-29 13:38:45,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf24a84-0819-48a6-b6c4-05839a047424/GCA_932190865.1_0308_S_metabat.018_genomic.fna.gz --refList GCA_932190865.1_0308_S_metabat.018_genomic.fna/target_genomes.txt --output GCA_932190865.1_0308_S_metabat.018_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:38:53,429] [INFO] Task succeeded: fastANI
[2023-06-29 13:38:53,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:38:53,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:38:53,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:38:53,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:38:53,434] [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 13:38:53,437] [INFO] DFAST Taxonomy check result was written to GCA_932190865.1_0308_S_metabat.018_genomic.fna/tc_result.tsv
[2023-06-29 13:38:53,438] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:38:53,438] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:38:53,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference/checkm_data
[2023-06-29 13:38:53,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:38:53,461] [INFO] Task started: CheckM
[2023-06-29 13:38:53,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_932190865.1_0308_S_metabat.018_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_932190865.1_0308_S_metabat.018_genomic.fna/checkm_input GCA_932190865.1_0308_S_metabat.018_genomic.fna/checkm_result
[2023-06-29 13:39:07,461] [INFO] Task succeeded: CheckM
[2023-06-29 13:39:07,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:39:07,482] [INFO] ===== Completeness check finished =====
[2023-06-29 13:39:07,482] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:39:07,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_932190865.1_0308_S_metabat.018_genomic.fna/markers.fasta)
[2023-06-29 13:39:07,483] [INFO] Task started: Blastn
[2023-06-29 13:39:07,483] [INFO] Running command: blastn -query GCA_932190865.1_0308_S_metabat.018_genomic.fna/markers.fasta -db /var/lib/cwl/stg4eb73f3c-e93e-447f-8ea4-7bd526a9627c/dqc_reference/reference_markers_gtdb.fasta -out GCA_932190865.1_0308_S_metabat.018_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:39:08,305] [INFO] Task succeeded: Blastn
[2023-06-29 13:39:08,310] [INFO] Selected 11 target genomes.
[2023-06-29 13:39:08,310] [INFO] Target genome list was writen to GCA_932190865.1_0308_S_metabat.018_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:39:08,324] [INFO] Task started: fastANI
[2023-06-29 13:39:08,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bf24a84-0819-48a6-b6c4-05839a047424/GCA_932190865.1_0308_S_metabat.018_genomic.fna.gz --refList GCA_932190865.1_0308_S_metabat.018_genomic.fna/target_genomes_gtdb.txt --output GCA_932190865.1_0308_S_metabat.018_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:39:12,704] [INFO] Task succeeded: fastANI
[2023-06-29 13:39:12,713] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:39:12,714] [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
GCF_000270205.1	s__Dwaynesavagella sp000270205	99.4491	226	250	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Dwaynesavagella	95.0	99.75	99.53	0.99	0.95	13	conclusive
GCF_000283555.1	s__Dwaynesavagella sp000283555	84.9631	207	250	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Dwaynesavagella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889345.1	s__Dwaynesavagella sp017889345	78.702	100	250	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Dwaynesavagella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655775.1	s__Dwaynesavagella gallinarum	78.5515	126	250	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Dwaynesavagella	95.0	99.29	99.12	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2023-06-29 13:39:12,716] [INFO] GTDB search result was written to GCA_932190865.1_0308_S_metabat.018_genomic.fna/result_gtdb.tsv
[2023-06-29 13:39:12,716] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:39:12,719] [INFO] DFAST_QC result json was written to GCA_932190865.1_0308_S_metabat.018_genomic.fna/dqc_result.json
[2023-06-29 13:39:12,719] [INFO] DFAST_QC completed!
[2023-06-29 13:39:12,719] [INFO] Total running time: 0h0m31s