[2023-06-17 14:43:10,854] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:43:10,864] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:43:10,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference
[2023-06-17 14:43:12,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:43:12,151] [INFO] Task started: Prodigal
[2023-06-17 14:43:12,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg5448aa32-6b8d-450f-90d3-c1c4b9357274/GCA_028680795.1_ASM2868079v1_genomic.fna.gz | prodigal -d GCA_028680795.1_ASM2868079v1_genomic.fna/cds.fna -a GCA_028680795.1_ASM2868079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:43:13,733] [INFO] Task succeeded: Prodigal
[2023-06-17 14:43:13,733] [INFO] Task started: HMMsearch
[2023-06-17 14:43:13,734] [INFO] Running command: hmmsearch --tblout GCA_028680795.1_ASM2868079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference/reference_markers.hmm GCA_028680795.1_ASM2868079v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:43:13,954] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:43:13,956] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5448aa32-6b8d-450f-90d3-c1c4b9357274/GCA_028680795.1_ASM2868079v1_genomic.fna.gz]
[2023-06-17 14:43:13,972] [INFO] Query marker FASTA was written to GCA_028680795.1_ASM2868079v1_genomic.fna/markers.fasta
[2023-06-17 14:43:13,972] [INFO] Task started: Blastn
[2023-06-17 14:43:13,972] [INFO] Running command: blastn -query GCA_028680795.1_ASM2868079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference/reference_markers.fasta -out GCA_028680795.1_ASM2868079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:15,514] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:15,522] [INFO] Selected 16 target genomes.
[2023-06-17 14:43:15,523] [INFO] Target genome list was writen to GCA_028680795.1_ASM2868079v1_genomic.fna/target_genomes.txt
[2023-06-17 14:43:15,556] [INFO] Task started: fastANI
[2023-06-17 14:43:15,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg5448aa32-6b8d-450f-90d3-c1c4b9357274/GCA_028680795.1_ASM2868079v1_genomic.fna.gz --refList GCA_028680795.1_ASM2868079v1_genomic.fna/target_genomes.txt --output GCA_028680795.1_ASM2868079v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:43:23,394] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:23,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:43:23,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:43:23,397] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:43:23,397] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:43:23,398] [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
--------------------------------------------------------------------------------
[2023-06-17 14:43:23,400] [INFO] DFAST Taxonomy check result was written to GCA_028680795.1_ASM2868079v1_genomic.fna/tc_result.tsv
[2023-06-17 14:43:23,400] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:43:23,401] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:43:23,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference/checkm_data
[2023-06-17 14:43:23,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:43:23,429] [INFO] Task started: CheckM
[2023-06-17 14:43:23,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028680795.1_ASM2868079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028680795.1_ASM2868079v1_genomic.fna/checkm_input GCA_028680795.1_ASM2868079v1_genomic.fna/checkm_result
[2023-06-17 14:43:38,056] [INFO] Task succeeded: CheckM
[2023-06-17 14:43:38,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:43:38,088] [INFO] ===== Completeness check finished =====
[2023-06-17 14:43:38,088] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:43:38,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028680795.1_ASM2868079v1_genomic.fna/markers.fasta)
[2023-06-17 14:43:38,089] [INFO] Task started: Blastn
[2023-06-17 14:43:38,089] [INFO] Running command: blastn -query GCA_028680795.1_ASM2868079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg805aa35a-b9f5-466a-8a2c-b8b4b00de6f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_028680795.1_ASM2868079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:38,874] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:38,878] [INFO] Selected 20 target genomes.
[2023-06-17 14:43:38,878] [INFO] Target genome list was writen to GCA_028680795.1_ASM2868079v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:43:38,900] [INFO] Task started: fastANI
[2023-06-17 14:43:38,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg5448aa32-6b8d-450f-90d3-c1c4b9357274/GCA_028680795.1_ASM2868079v1_genomic.fna.gz --refList GCA_028680795.1_ASM2868079v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028680795.1_ASM2868079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:43:43,643] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:43,649] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:43:43,650] [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_012520055.1	s__DUUS01 sp012520055	77.8811	116	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__DUUS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012841465.1	s__DUUS01 sp012841465	77.5676	74	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__DUUS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563275.1	s__CAG-533 sp004563275	77.2543	54	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533	95.0	96.32	96.32	0.86	0.86	2	-
GCA_905236935.1	s__CAG-533 sp905236935	76.3575	52	307	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-533	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:43:43,652] [INFO] GTDB search result was written to GCA_028680795.1_ASM2868079v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:43:43,653] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:43:43,657] [INFO] DFAST_QC result json was written to GCA_028680795.1_ASM2868079v1_genomic.fna/dqc_result.json
[2023-06-17 14:43:43,657] [INFO] DFAST_QC completed!
[2023-06-17 14:43:43,658] [INFO] Total running time: 0h0m33s