[2023-06-28 13:49:50,817] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:49:50,818] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:49:50,819] [INFO] DQC Reference Directory: /var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference
[2023-06-28 13:49:51,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:49:51,932] [INFO] Task started: Prodigal
[2023-06-28 13:49:51,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dd57138-3458-43ab-a220-9b260af3ced5/GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:49:53,702] [INFO] Task succeeded: Prodigal
[2023-06-28 13:49:53,702] [INFO] Task started: HMMsearch
[2023-06-28 13:49:53,702] [INFO] Running command: hmmsearch --tblout GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference/reference_markers.hmm GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:49:53,874] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:49:53,875] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4dd57138-3458-43ab-a220-9b260af3ced5/GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 13:49:53,889] [INFO] Query marker FASTA was written to GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 13:49:53,890] [INFO] Task started: Blastn
[2023-06-28 13:49:53,890] [INFO] Running command: blastn -query GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference/reference_markers.fasta -out GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:49:54,397] [INFO] Task succeeded: Blastn
[2023-06-28 13:49:54,400] [INFO] Selected 15 target genomes.
[2023-06-28 13:49:54,400] [INFO] Target genome list was writen to GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 13:49:54,404] [INFO] Task started: fastANI
[2023-06-28 13:49:54,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd57138-3458-43ab-a220-9b260af3ced5/GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:50:02,022] [INFO] Task succeeded: fastANI
[2023-06-28 13:50:02,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:50:02,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:50:02,024] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:50:02,024] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:50:02,024] [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 13:50:02,026] [INFO] DFAST Taxonomy check result was written to GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 13:50:02,026] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:50:02,026] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:50:02,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference/checkm_data
[2023-06-28 13:50:02,029] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:50:02,044] [INFO] Task started: CheckM
[2023-06-28 13:50:02,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 13:50:14,232] [INFO] Task succeeded: CheckM
[2023-06-28 13:50:14,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:50:14,251] [INFO] ===== Completeness check finished =====
[2023-06-28 13:50:14,251] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:50:14,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 13:50:14,251] [INFO] Task started: Blastn
[2023-06-28 13:50:14,251] [INFO] Running command: blastn -query GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgff680e26-5435-4f2c-9bf0-e3c9ddece583/dqc_reference/reference_markers_gtdb.fasta -out GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:50:14,891] [INFO] Task succeeded: Blastn
[2023-06-28 13:50:14,907] [INFO] Selected 16 target genomes.
[2023-06-28 13:50:14,907] [INFO] Target genome list was writen to GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:50:14,937] [INFO] Task started: fastANI
[2023-06-28 13:50:14,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dd57138-3458-43ab-a220-9b260af3ced5/GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:50:19,226] [INFO] Task succeeded: fastANI
[2023-06-28 13:50:19,231] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:50:19,232] [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_002707915.1	s__GCA-2707915 sp002707915	98.5913	241	329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.24	96.30	0.83	0.75	4	conclusive
GCA_902594545.1	s__GCA-2707915 sp902594545	78.3018	102	329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.77	99.77	0.82	0.82	2	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.3734	73	329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517565.1	s__GCA-2707915 sp902517565	77.3302	61	329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214065.1	s__GCA-2707915 sp004214065	76.6765	73	329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
--------------------------------------------------------------------------------
[2023-06-28 13:50:19,233] [INFO] GTDB search result was written to GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 13:50:19,234] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:50:19,236] [INFO] DFAST_QC result json was written to GCA_913048255.1_ERR599058_bin.67_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 13:50:19,237] [INFO] DFAST_QC completed!
[2023-06-28 13:50:19,237] [INFO] Total running time: 0h0m28s