[2023-06-30 20:06:34,604] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:06:34,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:06:34,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference
[2023-06-30 20:06:37,028] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:06:37,029] [INFO] Task started: Prodigal
[2023-06-30 20:06:37,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg942ea8d0-a731-4c45-afe4-024af621cef1/GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna.gz | prodigal -d GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/cds.fna -a GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:06:39,070] [INFO] Task succeeded: Prodigal
[2023-06-30 20:06:39,071] [INFO] Task started: HMMsearch
[2023-06-30 20:06:39,071] [INFO] Running command: hmmsearch --tblout GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference/reference_markers.hmm GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:06:39,291] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:06:39,293] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg942ea8d0-a731-4c45-afe4-024af621cef1/GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna.gz]
[2023-06-30 20:06:39,310] [INFO] Query marker FASTA was written to GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/markers.fasta
[2023-06-30 20:06:39,310] [INFO] Task started: Blastn
[2023-06-30 20:06:39,310] [INFO] Running command: blastn -query GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/markers.fasta -db /var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference/reference_markers.fasta -out GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:06:40,973] [INFO] Task succeeded: Blastn
[2023-06-30 20:06:40,978] [INFO] Selected 15 target genomes.
[2023-06-30 20:06:40,979] [INFO] Target genome list was writen to GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/target_genomes.txt
[2023-06-30 20:06:40,981] [INFO] Task started: fastANI
[2023-06-30 20:06:40,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg942ea8d0-a731-4c45-afe4-024af621cef1/GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna.gz --refList GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/target_genomes.txt --output GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:06:45,409] [INFO] Task succeeded: fastANI
[2023-06-30 20:06:45,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:06:45,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:06:45,414] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 20:06:45,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 20:06:45,414] [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
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	97.1275	74	79	95	conclusive
--------------------------------------------------------------------------------
[2023-06-30 20:06:45,416] [INFO] DFAST Taxonomy check result was written to GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/tc_result.tsv
[2023-06-30 20:06:45,417] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:06:45,417] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:06:45,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference/checkm_data
[2023-06-30 20:06:45,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:06:45,433] [INFO] Task started: CheckM
[2023-06-30 20:06:45,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/checkm_input GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/checkm_result
[2023-06-30 20:07:01,056] [INFO] Task succeeded: CheckM
[2023-06-30 20:07:01,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:07:01,081] [INFO] ===== Completeness check finished =====
[2023-06-30 20:07:01,081] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:07:01,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/markers.fasta)
[2023-06-30 20:07:01,082] [INFO] Task started: Blastn
[2023-06-30 20:07:01,082] [INFO] Running command: blastn -query GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/markers.fasta -db /var/lib/cwl/stg38653f1e-f8a6-4c29-8197-93dcd87c7e71/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:07:01,585] [INFO] Task succeeded: Blastn
[2023-06-30 20:07:01,590] [INFO] Selected 12 target genomes.
[2023-06-30 20:07:01,590] [INFO] Target genome list was writen to GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:07:01,593] [INFO] Task started: fastANI
[2023-06-30 20:07:01,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg942ea8d0-a731-4c45-afe4-024af621cef1/GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna.gz --refList GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/target_genomes_gtdb.txt --output GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:07:06,092] [INFO] Task succeeded: fastANI
[2023-06-30 20:07:06,098] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:07:06,098] [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
GCF_018881755.1	s__Polynucleobacter sp903953215	97.1275	74	79	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.19	97.38	0.93	0.86	15	conclusive
GCA_903843235.1	s__Polynucleobacter sp903843235	87.9081	63	79	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
GCA_903845455.1	s__Polynucleobacter sp903845455	83.33	66	79	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.50	98.25	0.75	0.69	7	-
GCF_018881925.1	s__Polynucleobacter sp903880555	83.1319	69	79	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	-
GCA_903858445.1	s__Polynucleobacter sp903858445	81.2472	60	79	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:07:06,100] [INFO] GTDB search result was written to GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/result_gtdb.tsv
[2023-06-30 20:07:06,101] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:07:06,103] [INFO] DFAST_QC result json was written to GCA_903830705.1_freshwater_MAG_---_E1_bin-458_genomic.fna/dqc_result.json
[2023-06-30 20:07:06,104] [INFO] DFAST_QC completed!
[2023-06-30 20:07:06,104] [INFO] Total running time: 0h0m31s