[2023-06-28 19:58:40,098] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:58:40,104] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:58:40,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference
[2023-06-28 19:58:41,619] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:58:41,620] [INFO] Task started: Prodigal
[2023-06-28 19:58:41,620] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa54f48c-47c1-48f6-88b6-36935ee9eabe/GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:58:46,998] [INFO] Task succeeded: Prodigal
[2023-06-28 19:58:46,998] [INFO] Task started: HMMsearch
[2023-06-28 19:58:46,998] [INFO] Running command: hmmsearch --tblout GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference/reference_markers.hmm GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:58:47,273] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:58:47,275] [INFO] Found 6/6 markers.
[2023-06-28 19:58:47,313] [INFO] Query marker FASTA was written to GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 19:58:47,314] [INFO] Task started: Blastn
[2023-06-28 19:58:47,314] [INFO] Running command: blastn -query GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference/reference_markers.fasta -out GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:58:47,953] [INFO] Task succeeded: Blastn
[2023-06-28 19:58:47,960] [INFO] Selected 23 target genomes.
[2023-06-28 19:58:47,961] [INFO] Target genome list was writen to GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 19:58:47,984] [INFO] Task started: fastANI
[2023-06-28 19:58:47,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa54f48c-47c1-48f6-88b6-36935ee9eabe/GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:58:58,634] [INFO] Task succeeded: fastANI
[2023-06-28 19:58:58,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:58:58,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:58:58,644] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:58:58,644] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:58:58,644] [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 19:58:58,647] [INFO] DFAST Taxonomy check result was written to GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 19:58:58,648] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:58:58,648] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:58:58,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference/checkm_data
[2023-06-28 19:58:58,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:58:58,699] [INFO] Task started: CheckM
[2023-06-28 19:58:58,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 19:59:21,848] [INFO] Task succeeded: CheckM
[2023-06-28 19:59:21,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:59:21,873] [INFO] ===== Completeness check finished =====
[2023-06-28 19:59:21,873] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:59:21,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 19:59:21,874] [INFO] Task started: Blastn
[2023-06-28 19:59:21,874] [INFO] Running command: blastn -query GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cbaa426-bb1a-48e4-a4ae-078a15873c25/dqc_reference/reference_markers_gtdb.fasta -out GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:59:22,857] [INFO] Task succeeded: Blastn
[2023-06-28 19:59:22,861] [INFO] Selected 14 target genomes.
[2023-06-28 19:59:22,861] [INFO] Target genome list was writen to GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:59:22,866] [INFO] Task started: fastANI
[2023-06-28 19:59:22,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa54f48c-47c1-48f6-88b6-36935ee9eabe/GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:59:28,338] [INFO] Task succeeded: fastANI
[2023-06-28 19:59:28,347] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:59:28,347] [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_002591625.1	s__TMED48 sp002591625	95.6607	604	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002701765.1	s__TMED48 sp002701765	93.6045	462	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	97.58	97.58	0.65	0.65	2	-
GCA_902557735.1	s__TMED48 sp902557735	79.5751	284	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692165.1	s__TMED48 sp002692165	79.3018	236	720	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-28 19:59:28,349] [INFO] GTDB search result was written to GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 19:59:28,350] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:59:28,354] [INFO] DFAST_QC result json was written to GCA_913044275.1_ERR599050_bin.116_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 19:59:28,354] [INFO] DFAST_QC completed!
[2023-06-28 19:59:28,354] [INFO] Total running time: 0h0m48s