[2023-06-30 20:45:15,527] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:45:15,530] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:45:15,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference
[2023-06-30 20:45:17,802] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:45:17,803] [INFO] Task started: Prodigal
[2023-06-30 20:45:17,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg570a24c7-479e-4196-8847-8641d48f554c/GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna.gz | prodigal -d GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/cds.fna -a GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:45:24,174] [INFO] Task succeeded: Prodigal
[2023-06-30 20:45:24,175] [INFO] Task started: HMMsearch
[2023-06-30 20:45:24,175] [INFO] Running command: hmmsearch --tblout GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference/reference_markers.hmm GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:45:24,392] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:45:24,394] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg570a24c7-479e-4196-8847-8641d48f554c/GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna.gz]
[2023-06-30 20:45:24,421] [INFO] Query marker FASTA was written to GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/markers.fasta
[2023-06-30 20:45:24,421] [INFO] Task started: Blastn
[2023-06-30 20:45:24,421] [INFO] Running command: blastn -query GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference/reference_markers.fasta -out GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:45:25,065] [INFO] Task succeeded: Blastn
[2023-06-30 20:45:25,070] [INFO] Selected 23 target genomes.
[2023-06-30 20:45:25,070] [INFO] Target genome list was writen to GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/target_genomes.txt
[2023-06-30 20:45:25,071] [INFO] Task started: fastANI
[2023-06-30 20:45:25,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg570a24c7-479e-4196-8847-8641d48f554c/GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna.gz --refList GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/target_genomes.txt --output GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:45:41,366] [INFO] Task succeeded: fastANI
[2023-06-30 20:45:41,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:45:41,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:45:41,369] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:45:41,369] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:45:41,369] [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
--------------------------------------------------------------------------------
[2023-06-30 20:45:41,371] [INFO] DFAST Taxonomy check result was written to GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/tc_result.tsv
[2023-06-30 20:45:41,372] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:45:41,372] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:45:41,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference/checkm_data
[2023-06-30 20:45:41,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:45:41,406] [INFO] Task started: CheckM
[2023-06-30 20:45:41,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/checkm_input GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/checkm_result
[2023-06-30 20:46:06,179] [INFO] Task succeeded: CheckM
[2023-06-30 20:46:06,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.64%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 20:46:06,204] [INFO] ===== Completeness check finished =====
[2023-06-30 20:46:06,204] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:46:06,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/markers.fasta)
[2023-06-30 20:46:06,205] [INFO] Task started: Blastn
[2023-06-30 20:46:06,205] [INFO] Running command: blastn -query GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b5a9a20-9c7a-4f6c-9062-4443763cb497/dqc_reference/reference_markers_gtdb.fasta -out GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:46:07,148] [INFO] Task succeeded: Blastn
[2023-06-30 20:46:07,153] [INFO] Selected 14 target genomes.
[2023-06-30 20:46:07,153] [INFO] Target genome list was writen to GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:46:07,177] [INFO] Task started: fastANI
[2023-06-30 20:46:07,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg570a24c7-479e-4196-8847-8641d48f554c/GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna.gz --refList GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/target_genomes_gtdb.txt --output GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:46:14,774] [INFO] Task succeeded: fastANI
[2023-06-30 20:46:14,785] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:46:14,785] [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_903896775.1	s__SHVO01 sp903896775	100.0	581	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903888485.1	s__SHVO01 sp903888485	77.9877	233	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694245.1	s__SHVO01 sp009694245	77.0457	124	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SHVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793005.1	s__GCA-2737725 sp016793005	76.8349	53	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297485.1	s__SCTM01 sp004297485	76.7499	87	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__SCTM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793085.1	s__GCA-2737725 sp016793085	76.7336	82	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869315.1	s__VGEM01 sp016869315	76.092	51	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__VGEM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693785.1	s__GCA-2737725 sp009693785	76.0672	54	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__GCA-2737725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:46:14,787] [INFO] GTDB search result was written to GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/result_gtdb.tsv
[2023-06-30 20:46:14,788] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:46:14,790] [INFO] DFAST_QC result json was written to GCA_903896775.1_freshwater_MAG_---_Umea_bin-03200_genomic.fna/dqc_result.json
[2023-06-30 20:46:14,790] [INFO] DFAST_QC completed!
[2023-06-30 20:46:14,790] [INFO] Total running time: 0h0m59s