[2023-06-28 18:16:51,422] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:16:51,425] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:16:51,426] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference
[2023-06-28 18:16:52,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:16:52,708] [INFO] Task started: Prodigal
[2023-06-28 18:16:52,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cd41e96-be4a-4f41-a071-b71ede64dd41/GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:16:58,505] [INFO] Task succeeded: Prodigal
[2023-06-28 18:16:58,505] [INFO] Task started: HMMsearch
[2023-06-28 18:16:58,505] [INFO] Running command: hmmsearch --tblout GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference/reference_markers.hmm GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:16:58,731] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:16:58,733] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7cd41e96-be4a-4f41-a071-b71ede64dd41/GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 18:16:58,764] [INFO] Query marker FASTA was written to GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 18:16:58,764] [INFO] Task started: Blastn
[2023-06-28 18:16:58,764] [INFO] Running command: blastn -query GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference/reference_markers.fasta -out GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:16:59,385] [INFO] Task succeeded: Blastn
[2023-06-28 18:16:59,389] [INFO] Selected 14 target genomes.
[2023-06-28 18:16:59,389] [INFO] Target genome list was writen to GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 18:16:59,395] [INFO] Task started: fastANI
[2023-06-28 18:16:59,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd41e96-be4a-4f41-a071-b71ede64dd41/GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:17:07,917] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:07,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:17:07,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:17:07,920] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:17:07,921] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:17:07,921] [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
--------------------------------------------------------------------------------
[2023-06-28 18:17:07,923] [INFO] DFAST Taxonomy check result was written to GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 18:17:07,924] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:17:07,925] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:17:07,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference/checkm_data
[2023-06-28 18:17:07,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:17:07,959] [INFO] Task started: CheckM
[2023-06-28 18:17:07,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 18:17:31,925] [INFO] Task succeeded: CheckM
[2023-06-28 18:17:31,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:17:31,950] [INFO] ===== Completeness check finished =====
[2023-06-28 18:17:31,951] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:17:31,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 18:17:31,951] [INFO] Task started: Blastn
[2023-06-28 18:17:31,952] [INFO] Running command: blastn -query GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0423c67-c5ba-476f-996e-646ad0b0d765/dqc_reference/reference_markers_gtdb.fasta -out GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:17:32,961] [INFO] Task succeeded: Blastn
[2023-06-28 18:17:32,968] [INFO] Selected 16 target genomes.
[2023-06-28 18:17:32,968] [INFO] Target genome list was writen to GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:17:32,981] [INFO] Task started: fastANI
[2023-06-28 18:17:32,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd41e96-be4a-4f41-a071-b71ede64dd41/GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:17:40,976] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:40,984] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:17:40,984] [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_002719135.1	s__UBA11889 sp002719135	98.5663	481	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.11	97.65	0.74	0.72	3	conclusive
GCA_002313255.1	s__UBA11889 sp002313255	93.2496	583	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.77	98.77	0.86	0.86	2	-
GCA_002715785.1	s__UBA11889 sp002715785	85.0204	475	651	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	99.18	99.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-28 18:17:40,987] [INFO] GTDB search result was written to GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 18:17:40,988] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:17:40,990] [INFO] DFAST_QC result json was written to GCA_913020175.1_ERR598999_bin.32_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 18:17:40,990] [INFO] DFAST_QC completed!
[2023-06-28 18:17:40,991] [INFO] Total running time: 0h0m50s