[2023-06-30 10:21:44,108] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:21:44,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:21:44,110] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference
[2023-06-30 10:21:46,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:21:46,026] [INFO] Task started: Prodigal
[2023-06-30 10:21:46,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d780833-ae0e-401b-aff8-69ef369f8ca3/GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna.gz | prodigal -d GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/cds.fna -a GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:21:56,293] [INFO] Task succeeded: Prodigal
[2023-06-30 10:21:56,293] [INFO] Task started: HMMsearch
[2023-06-30 10:21:56,293] [INFO] Running command: hmmsearch --tblout GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference/reference_markers.hmm GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:21:56,562] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:21:56,563] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9d780833-ae0e-401b-aff8-69ef369f8ca3/GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna.gz]
[2023-06-30 10:21:56,617] [INFO] Query marker FASTA was written to GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/markers.fasta
[2023-06-30 10:21:56,618] [INFO] Task started: Blastn
[2023-06-30 10:21:56,618] [INFO] Running command: blastn -query GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference/reference_markers.fasta -out GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:21:57,228] [INFO] Task succeeded: Blastn
[2023-06-30 10:21:57,233] [INFO] Selected 11 target genomes.
[2023-06-30 10:21:57,233] [INFO] Target genome list was writen to GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/target_genomes.txt
[2023-06-30 10:21:57,238] [INFO] Task started: fastANI
[2023-06-30 10:21:57,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d780833-ae0e-401b-aff8-69ef369f8ca3/GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna.gz --refList GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/target_genomes.txt --output GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:22:06,167] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:06,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:22:06,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:22:06,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:22:06,171] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:22:06,171] [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 10:22:06,174] [INFO] DFAST Taxonomy check result was written to GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/tc_result.tsv
[2023-06-30 10:22:06,174] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:22:06,175] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:22:06,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference/checkm_data
[2023-06-30 10:22:06,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:22:06,234] [INFO] Task started: CheckM
[2023-06-30 10:22:06,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/checkm_input GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/checkm_result
[2023-06-30 10:22:41,273] [INFO] Task succeeded: CheckM
[2023-06-30 10:22:41,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 10.69%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2023-06-30 10:22:41,301] [INFO] ===== Completeness check finished =====
[2023-06-30 10:22:41,301] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:22:41,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/markers.fasta)
[2023-06-30 10:22:41,302] [INFO] Task started: Blastn
[2023-06-30 10:22:41,302] [INFO] Running command: blastn -query GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb28f90b-8027-4bb5-a25d-a47ffb752a33/dqc_reference/reference_markers_gtdb.fasta -out GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:22:42,129] [INFO] Task succeeded: Blastn
[2023-06-30 10:22:42,133] [INFO] Selected 14 target genomes.
[2023-06-30 10:22:42,134] [INFO] Target genome list was writen to GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:22:42,167] [INFO] Task started: fastANI
[2023-06-30 10:22:42,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d780833-ae0e-401b-aff8-69ef369f8ca3/GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna.gz --refList GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/target_genomes_gtdb.txt --output GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:22:49,892] [INFO] Task succeeded: fastANI
[2023-06-30 10:22:49,900] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 10:22:49,900] [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_002347925.1	s__UBA12225 sp002347925	96.3081	697	819	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	98.21	95.05	0.90	0.85	18	conclusive
GCA_009693165.1	s__UBA12225 sp009693165	84.8132	392	819	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836285.1	s__CAILQO01 sp903836285	77.0179	134	819	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__CAILQO01	95.0	98.79	98.57	0.84	0.81	6	-
--------------------------------------------------------------------------------
[2023-06-30 10:22:49,902] [INFO] GTDB search result was written to GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/result_gtdb.tsv
[2023-06-30 10:22:49,903] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:22:49,906] [INFO] DFAST_QC result json was written to GCA_903832065.1_freshwater_MAG_---_Umea_bin-05786_genomic.fna/dqc_result.json
[2023-06-30 10:22:49,906] [INFO] DFAST_QC completed!
[2023-06-30 10:22:49,906] [INFO] Total running time: 0h1m6s