[2023-06-07 18:25:40,586] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:25:40,587] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:25:40,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference
[2023-06-07 18:25:41,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:25:41,862] [INFO] Task started: Prodigal
[2023-06-07 18:25:41,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ab38569-cbd2-48d1-b714-46bb911f67a7/GCA_945902045.1_MoE-02may19-224_genomic.fna.gz | prodigal -d GCA_945902045.1_MoE-02may19-224_genomic.fna/cds.fna -a GCA_945902045.1_MoE-02may19-224_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:25:48,930] [INFO] Task succeeded: Prodigal
[2023-06-07 18:25:48,930] [INFO] Task started: HMMsearch
[2023-06-07 18:25:48,930] [INFO] Running command: hmmsearch --tblout GCA_945902045.1_MoE-02may19-224_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference/reference_markers.hmm GCA_945902045.1_MoE-02may19-224_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:25:49,196] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:25:49,198] [INFO] Found 6/6 markers.
[2023-06-07 18:25:49,234] [INFO] Query marker FASTA was written to GCA_945902045.1_MoE-02may19-224_genomic.fna/markers.fasta
[2023-06-07 18:25:49,234] [INFO] Task started: Blastn
[2023-06-07 18:25:49,234] [INFO] Running command: blastn -query GCA_945902045.1_MoE-02may19-224_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference/reference_markers.fasta -out GCA_945902045.1_MoE-02may19-224_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:25:49,856] [INFO] Task succeeded: Blastn
[2023-06-07 18:25:49,862] [INFO] Selected 14 target genomes.
[2023-06-07 18:25:49,862] [INFO] Target genome list was writen to GCA_945902045.1_MoE-02may19-224_genomic.fna/target_genomes.txt
[2023-06-07 18:25:49,867] [INFO] Task started: fastANI
[2023-06-07 18:25:49,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ab38569-cbd2-48d1-b714-46bb911f67a7/GCA_945902045.1_MoE-02may19-224_genomic.fna.gz --refList GCA_945902045.1_MoE-02may19-224_genomic.fna/target_genomes.txt --output GCA_945902045.1_MoE-02may19-224_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:26:02,273] [INFO] Task succeeded: fastANI
[2023-06-07 18:26:02,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:26:02,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:26:02,277] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:26:02,277] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 18:26:02,277] [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
--------------------------------------------------------------------------------
[2023-06-07 18:26:02,279] [INFO] DFAST Taxonomy check result was written to GCA_945902045.1_MoE-02may19-224_genomic.fna/tc_result.tsv
[2023-06-07 18:26:02,279] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:26:02,280] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:26:02,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference/checkm_data
[2023-06-07 18:26:02,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:26:02,321] [INFO] Task started: CheckM
[2023-06-07 18:26:02,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945902045.1_MoE-02may19-224_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945902045.1_MoE-02may19-224_genomic.fna/checkm_input GCA_945902045.1_MoE-02may19-224_genomic.fna/checkm_result
[2023-06-07 18:26:30,126] [INFO] Task succeeded: CheckM
[2023-06-07 18:26:30,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:26:30,153] [INFO] ===== Completeness check finished =====
[2023-06-07 18:26:30,154] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:26:30,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945902045.1_MoE-02may19-224_genomic.fna/markers.fasta)
[2023-06-07 18:26:30,155] [INFO] Task started: Blastn
[2023-06-07 18:26:30,155] [INFO] Running command: blastn -query GCA_945902045.1_MoE-02may19-224_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f219811-7722-46f5-8ca1-14debafe91cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_945902045.1_MoE-02may19-224_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:26:31,000] [INFO] Task succeeded: Blastn
[2023-06-07 18:26:31,005] [INFO] Selected 25 target genomes.
[2023-06-07 18:26:31,005] [INFO] Target genome list was writen to GCA_945902045.1_MoE-02may19-224_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:26:31,017] [INFO] Task started: fastANI
[2023-06-07 18:26:31,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ab38569-cbd2-48d1-b714-46bb911f67a7/GCA_945902045.1_MoE-02may19-224_genomic.fna.gz --refList GCA_945902045.1_MoE-02may19-224_genomic.fna/target_genomes_gtdb.txt --output GCA_945902045.1_MoE-02may19-224_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:26:48,414] [INFO] Task succeeded: fastANI
[2023-06-07 18:26:48,419] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 18:26:48,419] [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_003670885.1	s__QWQI01 sp003670885	79.3225	251	799	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__QWQI01	95.0	97.74	97.58	0.93	0.88	4	-
GCA_016125085.1	s__RI-372 sp016125085	76.5081	89	799	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__RI-372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:26:48,421] [INFO] GTDB search result was written to GCA_945902045.1_MoE-02may19-224_genomic.fna/result_gtdb.tsv
[2023-06-07 18:26:48,422] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:26:48,424] [INFO] DFAST_QC result json was written to GCA_945902045.1_MoE-02may19-224_genomic.fna/dqc_result.json
[2023-06-07 18:26:48,424] [INFO] DFAST_QC completed!
[2023-06-07 18:26:48,424] [INFO] Total running time: 0h1m8s