[2023-07-01 06:37:39,410] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:37:39,415] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:37:39,416] [INFO] DQC Reference Directory: /var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference
[2023-07-01 06:37:40,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:37:40,672] [INFO] Task started: Prodigal
[2023-07-01 06:37:40,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg28633296-09ef-459e-adb5-d0a120f1b1e6/GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna.gz | prodigal -d GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/cds.fna -a GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:37:45,323] [INFO] Task succeeded: Prodigal
[2023-07-01 06:37:45,324] [INFO] Task started: HMMsearch
[2023-07-01 06:37:45,324] [INFO] Running command: hmmsearch --tblout GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference/reference_markers.hmm GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:37:45,530] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:37:45,532] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg28633296-09ef-459e-adb5-d0a120f1b1e6/GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna.gz]
[2023-07-01 06:37:45,578] [INFO] Query marker FASTA was written to GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/markers.fasta
[2023-07-01 06:37:45,578] [INFO] Task started: Blastn
[2023-07-01 06:37:45,578] [INFO] Running command: blastn -query GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/markers.fasta -db /var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference/reference_markers.fasta -out GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:37:46,130] [INFO] Task succeeded: Blastn
[2023-07-01 06:37:46,152] [INFO] Selected 16 target genomes.
[2023-07-01 06:37:46,153] [INFO] Target genome list was writen to GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/target_genomes.txt
[2023-07-01 06:37:46,157] [INFO] Task started: fastANI
[2023-07-01 06:37:46,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg28633296-09ef-459e-adb5-d0a120f1b1e6/GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna.gz --refList GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/target_genomes.txt --output GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:37:53,470] [INFO] Task succeeded: fastANI
[2023-07-01 06:37:53,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:37:53,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:37:53,472] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:37:53,472] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 06:37:53,472] [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
--------------------------------------------------------------------------------
[2023-07-01 06:37:53,478] [INFO] DFAST Taxonomy check result was written to GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/tc_result.tsv
[2023-07-01 06:37:53,479] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:37:53,479] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:37:53,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference/checkm_data
[2023-07-01 06:37:53,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:37:53,509] [INFO] Task started: CheckM
[2023-07-01 06:37:53,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/checkm_input GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/checkm_result
[2023-07-01 06:38:14,580] [INFO] Task succeeded: CheckM
[2023-07-01 06:38:14,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:38:14,602] [INFO] ===== Completeness check finished =====
[2023-07-01 06:38:14,603] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:38:14,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/markers.fasta)
[2023-07-01 06:38:14,604] [INFO] Task started: Blastn
[2023-07-01 06:38:14,604] [INFO] Running command: blastn -query GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/markers.fasta -db /var/lib/cwl/stga72032d3-3cd1-47e0-901f-bfd4dadad786/dqc_reference/reference_markers_gtdb.fasta -out GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:38:15,348] [INFO] Task succeeded: Blastn
[2023-07-01 06:38:15,365] [INFO] Selected 20 target genomes.
[2023-07-01 06:38:15,365] [INFO] Target genome list was writen to GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:38:15,403] [INFO] Task started: fastANI
[2023-07-01 06:38:15,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg28633296-09ef-459e-adb5-d0a120f1b1e6/GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna.gz --refList GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/target_genomes_gtdb.txt --output GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:38:24,574] [INFO] Task succeeded: fastANI
[2023-07-01 06:38:24,579] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 06:38:24,579] [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_903907185.1	s__CAIVND01 sp903907185	100.0	458	467	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__CAIVND01	95.0	99.81	99.81	0.92	0.92	2	conclusive
--------------------------------------------------------------------------------
[2023-07-01 06:38:24,597] [INFO] GTDB search result was written to GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/result_gtdb.tsv
[2023-07-01 06:38:24,598] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:38:24,600] [INFO] DFAST_QC result json was written to GCA_903907185.1_freshwater_MAG_---_Umea3_bin-0781_genomic.fna/dqc_result.json
[2023-07-01 06:38:24,600] [INFO] DFAST_QC completed!
[2023-07-01 06:38:24,601] [INFO] Total running time: 0h0m45s